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Darrin Fresh Water Institute,
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DFWI Research:

Adirondack Effects Assessment Program (AEAP)


The AEAP Program Table of Contents


The AEAP Program

The Aquatic Biota Study

The Aquatic Biota Study Components

Program Investigators and Personnel

Literature Cited





Brooktrout Lake, NY (photo: Jeremy Farrell)


Acid rain has been a problem throughout certain regions of the world for decades.  The problem is especially severe in the Northeastern United States due to emissions from coal-burning facilities in the mid-West and the general pattern of weather system movement from west to east.   Acid ion deposition from the atmosphere and subsequent leaching of metals from soil have affected surface waters in the Adirondack Region of New York State, particularly at higher elevations where soils are thin and natural buffering capacities are low.  Public concern over the acidification of lakes and ponds in the Adirondacks is focused on biological effects, primarily because of the use of these ecosystems for sport fishing.


The Clean Air Act Amendments

In 1990, Congress passed the Clean Air Act Amendments (CAAA), which mandated reductions in fossil fuel emissions to improve the quality of terrestrial and aquatic ecosystems.  The main target emissions were those that produced SOx and NOx which then convert in the atmosphere into sulfuric acid (H2SO4) and nitric acid (HNO3) and produce acid rain.  The reduction in SOx emissions was to take effect in 1994 while the reduction in NOx emissions would occur by 1998. 


The Adirondack Effects Assessment Program (AEAP)

The AEAP resulted from a 1992 Federal appropriation through Congress that was appended to the 1990 CAAA to support research on the effects of reduced air emissions, and RPI-DFWI was named as the primary recipient of the funding.  The AEAP was designed to provide comprehensive data of sufficient quantity and quality to evaluate directly the long-term response of biological communities to the reductions stipulated in the 1990 CAAA.  The specific design of the AEAP was an outgrowth of discussions at a Workshop of recognized experts held at RPI in January 1993.  Following the Workshop, which was Task 1 of the AEAP, the US EPA contract with RPI was modified to include three additional tasks (see below).  Subsequent work plans were reviewed internally by the US Environmental Protection Agency and by external peer reviewers.  

The AEAP Tasks

The RPI Workshop, described above, was the first Program task.  The remaining three tasks of the AEAP were as follows:

  • monitor status of aquatic biological communities in Adirondack waters (Aquatic Biota Study),
  • support continued monitoring of atmospheric deposition at the NADP sites in the Adirondack region (Huntington Forest and Bennett Bridge), and
  • perform research to determine the factors controlling the retention of atmospherically deposited nitrogen in Adirondack watersheds (Watershed Integrated Nitrogen Cycling Study).

dave winklerThe Aquatic Biota was initiated in 1994 and the Watershed Integrated Nitrogen Cycling Study was added in 1997.  The NADP sites in the Adirondacks had been in operation for several decades (Huntington Forest since 1978, Bennett Bridge since 1980) and received financial support to continue deposition monitoring during the period of the AEAP.

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The AEAP Components and Schedule


The AEAP was conducted within the Adirondack Park in New YorkState (Figure 1), and consisted of three distinct components: aquatic biota sampling, atmospheric deposition monitoring, and a study of watershed nitrogen cycling.  The Aquatic Biota Study included water chemistry and aquatic biota sampling, and was initiated in 1994.  From 1994 through 1996, a total of 30Program waters (click for map) were sampled three times each summer.  Starting in 1997, and continuing through 2005, the study waters were sampled twice each summer.  During 2002, an additional five waters were added to the 30 original Program study sites. 



Figure 1. Adirondack Park in New York


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bob bombardThe Aquatic Biota Study


Study Goals

A major conclusion of the 1993 RPI Workshop discussions was that significant knowledge gaps existed in understanding of the effects of acidification on aquatic organisms and, furthermore, that the lack of consistent biological data collection would make it difficult to assess whether lake communities are changing over time.  Accordingly, the goals of the AEAP Aquatic Biota Study were structured to:


  • provide long-term (temporal) benefits by collecting baseline information that could be used to evaluate the future recovery of lake communities, and
  • provide short-term benefits in the increased understanding of the complex effects of acidification on community structure by simultaneously evaluating effects of acidification on multiple trophic levels in multiple types of lake systems.

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Study Objectives

The objectives that were developed for the Aquatic Biota Study are as follows:

1)    quantify the interactive relationships between environmental factors and species abundance within the bacterioplankton, phytoplankton, zooplankton, macrophyte, and fish communities.
2)    evaluate species within the bacterioplankton, phytoplankton, zooplankton, macrophyte, and fish communities as indicators of acidification to provide a basis for assessing recovery from acidification.
3)    categorize study waters into distinct types based on the abundance and assemblage of indicator species and physical/chemical ecosystem characteristics; compare categories based on indicator species and physical/chemical attributes and use categories to set target levels for recovery.
4)    document shifts of waters from categories typical of acidification to categories typical of unaffected lakes if recovery is occurring.
5)    detect association between trends of recovery (shifts of lakes between categories) and reductions in acidic atmospheric deposition.

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aeap fieldStudy Design 

The Aquatic Biota Study was designed to provide 1) baseline data upon which to evaluate temporal changes, and 2) short-term gains in understanding the effects of acidification on ecosystem community structure. The specific challenges of designing the Study to meet these goals were as follows:

  • logistical constraints of sampling statistically significant numbers of ponded waters to provide adequate monitoring data,
  • providing an adequate diversity of study sites to cover the different lake types encountered in the Adirondacks and the wide geographic area encompassed by the Adirondack Mountain region,
  • providing a statistically defensible number of replicates that would allow analyzing trends in space and time, and
  • conducting adequate sampling of multiple trophic levels to allow the analysis of complex effects of acidification and to distinguish between the effects of acidification and other factors.

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Study Region and Sites (click on a pin to obtain lake name)


View AEAP in a full screen map (pins represent actual sampling point on lake)

In order to meet the objective of detecting temporal changes in biological community structure, the Study region for the AEAP was limited to the southwest portion of the Adirondack Park.  The primary considerations for this selection were that

  • this region of the Adirondack Park receives the highest deposition rates of air-borne pollutants originating in the Ohio Valley,
  • lakes and ponds in this region are the most impacted, and may be most likely to demonstrate the effects of recovery, and
  • restricting the area of the Study decreases geographic and climatic variability that may tend to increase variance and decrease the statistical power to detect temporal change.

To meet the second objective of the research and evaluation effort, the AEAP Study sites (lakes and ponds) were selected to incorporate different hydrologic types including

  • thin till, drainage, low dissolved organic carbon (DOC)
  • thin till, drainage, high DOC
  • medium till, drainage, low DOC
  • medium till, drainage, high DOC
  • mounded, seepage, low DOC
  • mounded, seepage, high DOC
  • carbonate
carry pond
Carry Pond (Photo: Scott Quinn)

This categorization of ponded waters was based on the classification scheme developed by Newton and Driscoll (1990) and was used by other researchers in the Adirondack Region.

Finally, to provide the highest degree of accuracy in relating spatial and temporal biological characteristics to lake and pond water chemistry, the Study sites were selected to coincide with an on-going water chemistry monitoring program, the Adirondack Long-Term Monitoring (ALTM) Program, which was initiated in 1992 and sampled the water chemistry of 52 lakes and ponds monthly.

The focus of the Aquatic Biota Study on the southwest Adirondack region 1) allowed the assessment of recovery where acidification is most prevalent and where the fish communities are most affected, 2) resulted in decreased variability among lakes and ponds by including waters within a smaller region, and 3) increased the ratio of sampled to total waters in the study region, allowing the extrapolation of the results to the larger region affected by acidification.

The 35 ponded waters included in the Aquatic Biota Study are listed in Table 1 and located on a map in Figure 1.  The listing includes the original 30 waters and the five additional waters added to the Program in 2002.  Some of the 35 waters have been included in other Adirondack research programs.

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Table 1. List of study sites sampled during the Aquatic Biota Study, 1994-2006.  The number listed under “Code” is the map location of the water body on Figure 1
































































































































































































































































































































1 W# = watershed number, i.e., the major drainage basin within which the ponded water is located.  There are 17 major watersheds in New York State (“04” = Oswegatchie/Black, “05” = Upper Hudson, “06” = Raquette, “07” = Mohawk/Hudson)

2 P# = pond number, i.e., the number designated for a specific ponded water by the NYSDEC in Part 800 of Codes, Rules and Regulations pertaining to Article 15 of the NYS Environmental Conservation Law

3 Hydrologic Type is explained in the text of the document


dave winklerSampling Frequency

Budgetary constraints associated with the AEAP required balancing the sampling frequency with the total number of ponded waters that were sampled.  The lakes and ponds were sampled three times during 1994, 1995 and 1996 to facilitate statistical analysis, and the three sampling intervals were conducted during the summer period of thermal stratification (between mid-June and mid-September) to provide the lowest variance within the ecosystem.  

Although the biological communities sampled during the summer season may not exhibit the direct impacts of episodic acidification associated with spring snowmelt and runoff (which can be a major effect of acid precipitation), replication of sampling during the most stable part of the growing season increases the ability to detect temporal changes in the long-term effects of acidification.  The Study would not have been able to sample both spring and summer seasons adequately, and spring sampling is problematic (more variable, logistical problems associated with snowmelt and ice-out, unpredictable weather and hydrologic conditions).  It was anticipated that by replicating sampling during summer, the lakes would be stratified and biological communities would be relatively stable.  The summer data can be used to assess inter-annual variability, rather than seasonal variability and, hopefully, to evaluate differences in biological community structure among lake types and detect changes over time.

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Program Scheule

Extension of the AEAP beyond 1996 required renegotiation of the Program work plan and approval by the US EPA and external peer reviewers.  Following this process, US EPA mandated a reduction of the budget for the Aquatic Biota Study.  In order to accommodate the budget reductions and also minimize the impact of these reductions on the ability to detect temporal changes in aquatic biota, the frequency of Study sampling was reduced to twice each summer, rather than reduce the total number of lakes and ponds being studied.

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do meterSample Types.

The Aquatic Biota Study collected water chemistry samples, depth profiles of temperature, dissolved oxygen and light, and samples for bacterioplankton, phytoplankton, zooplankton, macrophytes, and fish (Table 2). 

Water samples were collected at the time of sampling for bacterioplankton, phytoplankton, and zooplankton, in order to provide contemporaneous water chemistry information.  All of these different types of samples were collected during each mid-summer sampling period.  Sampling for fish and macrophytes was more time consuming and labor intensive and, therefore, was conducted at different times.  The following material is a brief summary of activities for the various types of samples that were collected:

  • Water Chemistry: water samples were collected at each study site coincident with the collection of the mid-summer biological samples.  Two samples (epilimnetic and hypolimnetic) were collected from waters that exhibited thermal stratification; a single sample (epilimnetic) was collected from waters that were not thermally stratified.  The water samples were processed, preserved (where appropriate) and analyzed for the chemicals and nutrients presented in Table 3.
  • Bacterioplankton: sub-samples were taken from an integrated epilimnetic and a single depth hypolimnetic (1m off the bottom) collection and filtered through 0.22µm filters (5 mL for microscopy and approximately 900-1000 mL for either DNA or RNA).  The filters were preserved for microscopy or frozen at –80oC for subsequent DNA and RNA extractions to identify bacterial species from 16S ribosomal DNA and 16S ribosomal RNA sequences.    
  • Phytoplankton: single sub-samples (300 mL) were collected from the water column down to the depth of 1% light penetration (using the integrated hose technique), preserved, and examined by light microscopy.
  • Zooplankton: samples were collected from the water column using a hose integration technique, a pump and a 64-µm mesh net (described in the QA/QC document).  The samples were narcotized, preserved, and examined by light microscopy.  Two zooplankton samples were collected during each site visit. 
  • Macrophytes: communities were observed and data recorded by SCUBA divers who followed transects from the shoreline to the extent of the littoral zone.  
  • Fish: these communities were sampled using trap nets and tag-and-recapture methods.  Sampling occurred during the spring and fall each year on a regular subset of study sites (Moss Lake, Dart Lake, Lake Rondaxe).  During the period 1994-2005, other waters were selected for survey using the conventional techniques, and waters with difficult access were surveyed with snorkeling. 

Table 4 summarizes the scope of components included in the AEAP Aquatic Biota project during Phase I (1994-1996), Phase II (1997-2002), and Phase III (2003 thru 2006).


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Sampling Schedule

Every year, the AEAP waters were sampled synoptically during each period to minimize variability and allow comparison of the biological data among waters.  Each sampling period consisted of two 2-3 day intervals during consecutive weeks.  One week was devoted to sampling remote waters by aircraft; waters accessible by land were sampled during the other week.  A total of 5-8 lakes and ponds usually were sampled each day. 

Sampling Regime

Each day, two sampling crews, each consisting of 2 people, sampled the designated waters, returning to the field laboratory during the day with samples collected from 2-3 sites for processing.  At each lake or pond site, the sampling crew positioned a boat or canoe at the location of maximum depth (using bathymetric maps and an electronic depth sounder), and collected depth profiles of temperature, light, and oxygen.  Epilimnetic water samples were collected using a wide-diameter hose to provide a depth-integrated composite for chemistry; a hypolimnetic grab sample was collected from 1.0 m above the bottom using a Van Dorn sampler.  Water also was collected from the surface to the depth of 1% light intensity using the integrate hose to sample phytoplankton.  Zooplankton were collected by slowly lowering the 2.54 cm ID diameter hose from the surface to 1.0 m above the bottom and pumping the water through a 64 um zooplankton net as the hose traverses the water column.  All collected water samples were stored on ice until delivery to the field laboratory.  The phytoplankton and zooplankton samples were preserved in the field.

The laboratory crew, consisting of 3-4 people, works in the field lab located at Eagle Bay, NY.  All samples are immediately accessioned upon delivery to the field lab.  Then, the samples were processed and either refrigerated and stored until delivery to the Keck Water Lab in Troy, NY, or immediately analyzed in the field lab (conductivity, chlorophyll a, conductivity, ammonium and soluble phosphorus).


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A detailed description of protocol and methodology for the Aquatic Biota Project was prepared in the QA/QC (Quality Assurance/ Quality Control) document that was submitted to US EPA and approved prior to implementation of the Program (Rensselaer Polytechnic Institute, 1994).

Data Entry, Handling, and Storage

A description of data entry, handling and storage for the Aquatic Biota Project is presented in the Quality Assurance (QA/QC) document that was submitted to US EPA and approved prior to implementation of the Program.

Summary of Study Accomplishments - Results through 2006. 

The following information is a summary of accomplishments and results of the Aquatic Biota Study during the period from 1994 through 2006. The written material provided in the following sections is the Significant Findings section of each chapter prepared for the Final Report that describes the results of this 13-year study.  For a more thorough presentation of study results, the reader is referred to the AEAP Final Report in its entirety (Nierzwicki-Bauer et al. 2008).

Sampling of Ponded Waters

During the 13-year duration of the Program, every effort was made to sample Program waters in as brief a time period as possible (synoptic sampling) during each sampling interval.  Except for the first sampling interval in June 1994 that required 32 days to complete, the suite of lakes and ponds generally were sampled within a 7-10 day period.  Examination of the water temperature versus depth profiles collected on each body of water on every sampling date confirmed that all waters were sampled during the period of thermal stratification, thus minimizing the variability of ecosystem factors that affect the stability of the mid-summer biotic communities.   

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The Aquatic Biota Study Components


Water Chemistry

Site Set Chemistry Comparisons and TrendsPrior to a detailed statistical analyses of all study data, exploratory evaluation of specific analyte concentration changes, and trends with respect to study site set pH and ANC was performed.  Presented here is an overview of findings specific to comparisons of overall changes in specific analyte concentrations from 1994 to 2006, trends in pH and ANC across the study, and changes site category, based on pH and ANC, across the study.

Across the study, overall positive gains were noted in pH, with the largest increases occurring in seepage sites, and the largest decreases in sites with high DOC content.  No general increase in study site set ANC was found, but the largest gains occurred in seepage sites, with high DOC sites showing the greatest losses.  Sulphate concentrations showed universal decreases across the study sites, with the largest decreases evident in the carbonate, seepage, and high DOC sites.  Nitrate concentrations also decreased across the study, with the largest decrease most prevalent in thin tilled, drainage sites.

Comparisons of sample types, epilimnetic and hypolimnetic, revealed distinct differences with respect to pH and ANC.  Hypolimnetic samples showed higher conserved pH and ANC across the study.  Changes in pH varied between the sample types across the study and with respect to annual changes; the majority of annual pH gains in epilimnetic samples were nullified by substantial decreases in study site set pH that occurred in sample years 2002, 2003, and 2006. Gains in study site set ANC were greater in hypolimnetic samples than in epilimnetic samples, which showed an overall loss of 1.21 ueq/L for the study.  Substantial decreases in epilimnetic site set ANC were noted for 1996, 2000, 2003, and 2006. 

Grouping of the study sites into pH and ANC categories revealed net reductions in sites with pH values less than 4.5, net gains in sites with pH values greater than 6.0, a decrease in study sites exhibiting ANC values greater than 50.0 ueq/L, and decreases in study sites with ANC values less than 0.0 ueq/L, across the duration of the study.

Water Chemistry and Chlorophyll aTrend analyses of water chemistry and chlorophyll a for 30 AEAP sites was completed on epilimnetic water samples across the sampling years of 1994-2003.  The findings of these analyses are published in Momen et al. (2006).  Significant findings of this work included (1) increases in pH in 83% of the AEAP sites (P<0.05), (2) increases in acid-neutralizing capacity (ANC) in 40% of the sites (P<0.05), (3) decreases in concentrations of both SO42− and Mg2+ in 37% of the sites (P<0.05), and (4) decreases in concentrations of NO3− (67% of sites, P<0.05) and NH4+ (33% of sites, P<0.05; 43% of sites, P<0.1).  Concentrations of inorganic and organic monomeric aluminum generally were below the reporting limit of 1.5 μmol L−1, but decreases were detected in four and five sites, respectively (P<0.1).  Concentrations of chlorophyll a increased in seven sites at a significance level of P<0.05 and two sites at a significance level of P<0.1. A significant inverse correlation also was found between chlorophyll a and NO3− concentrations in nine sites at a significance level of P<0.05 and two sites at a significance level of P<0.1. Overall, the results suggest (a) a degree of chemical recovery from acidification during the summer, (b) an increase in phytoplankton productivity, and (c) a decreasing trend in NO3− concentrations resulting from the increased productivity.

waterchemStratification and Water ChemistryFollowing the completion of the 2003 season, a series of statistical analyses were performed to evaluate whether differences existed between samplings performed during different stratification regimes, and between epilimnetic and hypolimnetic chemistry data during periods of stratification.  Periods of stratification generally had lower ANC, NH4+, Mg2+, Na+, K+, Ca2+, Cl-, and pH.  This analyses revealed that periods of stratification universally showed higher concentrations for all Al fractions, and for most sites, also showed higher SO42- and NO3- concentrations. 
With respect to differences between water layer chemistry, hypolimnetic sample concentrations for all analytes, except SO42- and NO3-, generally were equal to or greater than epilimnetic sample concentrations.  The largest differences were observed for Fe, NH4+, and DIC, which generally were 500 to 1100% higher in the hypolimnion than in the epilimnion.  Hypolimnetic concentrations of MRP, ANC, TP, and chlorophyll a also were substantially higher in the hypolimnion, generally by about 150 to 300%.  Lake water SO42- concentrations generally were lower in the hypolimnion, perhaps reflecting the importance of in-site sulfate reduction processes at low dissolved oxygen concentrations.

In addition, strong positive correlations were found between dissolved oxygen (DO) and each of the mineral acid anions potentially derived from atmospheric deposition (NO3- and SO42-).  Strong negative correlations were found between DO and NH4+, DIC, and Fe.  These relationships were evident across all samples combined; however, a strong negative correlation between dissolved oxygen and sample layer also was noted.  Hypolimnetic samples showed strong positive correlations of DO with NO3- and SO42-, and strong negative relationships with NH4+ and DIC.  Epilimnetic samples revealed a negative relationship with respect to Fe, and positive correlations with Cl- and MRP.  These findings suggest that many of the previously stated stratification differences may be attributable to DO content. 

pHmeterDifferences also were noted for several key water chemistry analytes with respect to whether or not a site was stratified during sampling.  Differences in NH4+, Chl a and DIC between epilimnetic and hypolimnetic samples may be attributable to microbial mediated decomposition in hypolimnetic waters.  Differences with respect to Fe, TP, and MRP are likely related to increased solubility under low oxygen conditions (Wetzel 1975), with many of the trends noted dependent not only on reduced oxygen levels, but the specific concentrations of modifiers such as DIC, SO42-, Fe, and ANC.  Higher hypolimnetic sample concentrations of NH4+, DIC, Mg2+, and K+ may have resulted from strong negative correlations to oxygen levels, suggesting these may be related to oxygen depletion.  In addition, NO3- and SO42- differences appear to be derived from positive correlations with oxygen in hypolimnetic samples, with no apparent correlations evident in epilimnetic samples.  Observed differences in TP, MRP, ANC and Fe are not conclusively linked to oxygen depletion as correlations were found in both layers and in the combined analysis; however, research has shown direct correlations between these analytes and hypolimnetic layer processes such as microbial anaerobic metabolism, increased solubility under low oxygen conditions, and in-situ alkalinity generation processes.  Noted differences with respect to aluminum fractions and Chl a do not appear related to oxygen depletion in hypolimnetic waters.  Higher levels of DIC and Chl a are most likely the product of gravity-induced settling of epilimnetic-derived organics.

Data QualityProcedures to evaluate the integrity and quality of the chemistry database were applied in two stages.  The first stage, performed following the 2003 season, rigorously evaluated data collected between 1994 and 2003.  Test parameters included titrated versus calculated ANC, measured versus calculated conductivity, cation and anion balances, pH, and yearly conductivity and ANC balances.  These tests were performed on epilimnetic and hypolimnetic data.  In May of 2007, a similar but less comprehensive evaluation was performed on epilimnetic data from 2004-2006.  Tests results, coupled with statistical evaluation of standard deviations, were used to identify any outliers or potential areas of analyses errors.  Following identification, all outliers were individually evaluated and decisions made for possible corrective measures. 
Significant findings of this work included adherence to expected standards for yearly conductivity, anion/cation balance, and measured versus calculated ANC and conductivity, for corrected epilimnetic and hypolimnetic data from 1994-2003 and epilimnetic data from 2003-2006.  Multiple regression equations were successfully created and applied to correct Ca values from 1994-1999, which had been determined without the addition of Lanthanum prior to analyses.  Abnormalities were identified and corrected with respect to anion determinations in 1998-1999, chl a data for 2001-2006, and various other analyte outliers from 1994-2006.  In addition, specific format, analyses, and corrective procedures were drafted and employed to ensure the efficacy of the final data product.

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The long-term objective of this component was to develop molecular probes specific for bacterial types found in the water and identified through their nucleic acid sequences.  Once developed, they could be used for rapid assay of microbial communities.  Ultimately, the effects of acidification on microbial communities could be determined by using genetic information derived directly from populations in the AEAP study sites.  Since this approach required a large sample size and is time-consuming, work prior to 2002 was limited to 16S ribosomal DNA sequence data obtained from bacterial clones sampled from only six of the original 30 ponded waters.  In work done before 2002, four oligo-nucleotide probes were designed, experimentally tested, and used in conjunction with slot blot hybridizations (Hiorns et al., 1997; Methe et al., 1998).

Samples were collected in 2005 for all 35 study sites during July and August for the epilimnion and hypolimnion layers (when both layers were present).  Also during 2005, cloning and sequencing was completed for 26 study sites sampled in 2002.  In addition, cloning and restriction fragment length polymorphisms (RFLP’s) of 2003 samples (July and August sets) were finished on four sites (Brooktrout Lake epilimnion and hypolimnion layer for July sampling; Brooktrout Lake epilimnion layer for August sampling; Carry Pond epilimnion layer for August sampling; North Lake epilimnion layer for August sampling; Sagamore Lake epilimnion and hypolimnion layer for August sampling).  No sequencing was done on 2003 samples except the Brooktrout Lake August epilimnion layer.

Kodak 1D Image Analysis Software Version 3.6 (Eastman Kodak, Rochester, NY) was used to analyze digital images of RFLP patterns which were fractionated in agarose gels.  Sizes of the restriction fragments were calculated with Kodak 1D by comparing their migration distances to the migration distance of fragments of known sizes in standard molecular weight marker DNA.  Restriction fragment size data then was exported to Microsoft Excel (Microsoft, Redmond, WA) for sorting and frequency analysis of the RFLP patterns.  This procedure was implemented for a total of 18 sites, 17 sites sampled in 2002 and one site sampled in 2003.

Phylogenetic trees were constructed for 16 study sites, which included only the 5 most abundant species found in each phylogenetic group. The sites included Big Moose, Brooktrout, Carry, Cascade, Dart, Grass, Helldiver, Icehouse, Indian, Long, Moss, North, Sagamore, Willis, Willy’s and Windfall.  Table 6 lists the five most abundant species found in these sites. 

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Phytoplankton Studies

In the earlier years of the AEAP, there were low densities and very few taxa (less than 10).  In 1998, coccoid blue-greens began to increase, probably peaking by 2000.  The number of taxa increased slightly (since 1999 the average ranged around 10-12) but flucuated considerably on a seasonal basis. The Dinobryon species and dinoflagellates still were important taxa, however.  The large dinoflagellates (like Peridinium limbatum and P. wisconsinse), however, had reduced populations; Peridinium inconspicuum, a small dinoflgellate, still was an important member of the Brooktrout phytoplankton assemblages.

As was noted for the Brooktrout Lake data and for other lakes in previous years (through 1998), the number of algal species generally increased over time, but with much seasonal and spatial variability.  There were several samples in 1999 and 2000 that had a greater number of taxa than previous years (up to 30 taxa in a sample).  Additionally, there were fewer samples with only large dinoflagellates.

As alluded to above, the abundance of dinoflagellates (mostly species of Peridinium) changed over the years, but still were an important portion of Adirondack Lake phytoplankton communities.   The larger forms were replaced by the smaller, more abundant forms, and assemblages with only large dinoflagellate forms were rare.  The large forms still were common, sometimes in abundant numbers, however they were associated with common forms of chyrsophytes, greens and blue-greens.

The increased numbers of unicellular coccoid blue-greens found in the Brooktrout samples (peaking in 2000) was not as abundant as in other Adirondack Lakes.  However, other coccoid species (usually colonial forms like Merismopedia and Microcystis) were important components of Adirondack phytoplankton assemblages, especially in the later (seasonally) samples.

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Zooplankton Studies

jeremy farrellMicrocrustaceans and rotifers were examined from 30 Adirondack sites from 1994-2006 as part of the AEAP.  The goal of this effort was to generate baseline data to assess biotic recovery should water column pH of the study sites rise, which was expected to occur as a result of the 1991 Clean Air Act Amendments.  The 28 species of microcrustaceans and 53 species of rotifers identified from these sites displayed differential sensitivity to acidic conditions and showed direct correlations of species richness, diversity and evenness with pH that was readily apparent during 1994-1996, the most acidic period during the study.  Biotic recovery is expected to follow chemical recovery at some point in time.  Since there was considerable variation in pH between collections and collection years, pH change was evaluated by comparing the average pH of sites from the first three (3) years (1994-1996) and the last three (3) years (2004-2006) of the study.  Only 10 sites showed a pH increase >0.4 units during the 13 year period and only five (5) sites exceeded pH 6.0, a critical level where community changes are believed to occur.  Acid sensitive species were identified by Detrended Correspondence Analysis (DCA) and by the lowest pH of occurrence in the 30 study sites.  Changes in species richness, biodiversity and densities of acid sensitive species were used to evaluate biotic recovery in sites exhibiting pH improvement.  Regression analysis revealed only minor changes in community variables relative to pH or elapsed time in three (3) sites for microcrustaceans and five (5) strong and four (4) weak changes for rotifers in nine (9) sites. There was a strong change for microcrustaceans alone in a 10th site.  It appears that very little chemical or biotic recovery has occurred in these sites to date.  Furthermore, there is evidence that the trajectory of chemical improvement may have stalled during the last three (3) years of the study (2004-2006).  The lowest average mid-summer pH of all 30 study sites since 2000 occurred in 2004 and 2006, and 6 of the 10 sites showing pH improvement lost an average 0.23 pH units since 2003.  The continued long-term monitoring of these study sites is critically important and recommended since it is important to know how the trajectory of improvement has changed and its effects on biotic recovery.

zoobottlesMicrocrustaceans and rotifers showed reduced species richness and diversity across the range in acidity of the AEAP study sites during the period, 1994-1996.  Acid tolerant species made up 44 percent of the microcrustaceans and 40 percent of the rotifers observed during the 13 years of collections.

The evidence of chemical recovery in the AEAP sites was sparse and incomplete.  The average pH of the 30 study sites varied between 0.1 and 0.3 units among years; there were only four (4) sites that had an average pH improvement of 0.5 units and nine (9) sites that had an average pH improvement of 0.4 units in 2004-2006, compared to values during 1994-1996.  Not counting the 10 sites that had pH>6.0 in 1994-1996, and two (2) sites that are acidic with high humic acids, there still were 13 sites that remained below the critical level of pH 6.0 by 2006.

The evidence for biotic recovery was sparse and incomplete.  Regression analysis revealed significant changes in some community composition variables in 10 sites; these changes were highly significant in only 5 sites.  The biotic recovery responses were limited to those sites exhibiting at least 0.4 units of pH improvement and did not occur at all in at least two of those sites.  There were a greater number of significant regression responses with community variables with the rotifers than with the crustaceans.

We introduced the community composition index as a relatively rapid method to identify communities experiencing acidification stress and to monitor lakes for biotic recovery over time.  All three (3) of the community indices, crustacean, rotifer and phytoplankton, should be applicable to acidification studies in other regions of the world with some modification to accommodate endemic species.

The zooplankton community results presented here following 13 years of investigation demonstrate, quite clearly, that biotic recovery is a continual process and not a static endpoint that is achieved following some period of time.  It also is apparent that the AEAP study sites require more time to demonstrate significant biotic recovery.  From the present perspective, 13 years of investigation is not nearly enough time for data collection to evaluate the effectiveness of the 1991 Clean Air Act Amendments.  Furthermore, the trajectory of chemical improvement noted through 2003 may have stalled. It is important to know if this apparent stasis is the result of random variation or represents the establishment of a new equilibrium. It is imperative that collections continue at the 30 AEAP sites in order to fully realize the implications of recovery from acidification.

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Macrophyte Studies

Seven hundred and sixty three (763) macrophyte specimens including 64 species have been identified and archived from thirty-one sites as part of the AEAP database.  The sites ranged in pH from 4.71 to 7.80 (s.u.), and contained an average of 14.3(±1.3) species per lake, which is comparable to low elevation, moderately productive lakes in New York State (15 species; Taggett et al. 1990).  Drainage lakes produced a substantially greater number of species per lake (15.5±1.5) than seepage lakes (6.5±1.8).  In general, aquatic plants were distributed from the lakeshore (emergent species) to a maximum depth of about 7 meters.  In several sites, specimens of the bladderwort, Utricularia purpurea, were found as deep as 12 meters.  Deep-water range extension is commonly observed in weakly rooted species such as the bladderworts; however, these specimens rarely survive to the next growing season.

The AEAP has provided an opportunity to build the largest aquatic plant database for the entire Adirondacks.  Future work on the recovery of these aquatic resources should include the monitoring of aquatic plants, as the lakes themselves show continued potential for recovery.  The reintroduction of circumneutral species should be followed with the concomitant reintroduction of fish that depend vitally on a diverse and more complex littoral zone than their acid-impacted counterparts.

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Fisheries Investigations

AEAP fishThe twelve years of fish data collected from the AEAP sites provides a wealth of information on the structure of fish assemblages in these sites and on their abundance and relative abundance.  The series of twice-annual collections in three sites (Dart, Moss and Rondaxe) is particularly useful in providing information on changes in assemblages.

Fish abundance, richness, diversity and other assemblage-level measurements may not be particularly useful in assessing the effect of, or changes in the effect of, water chemistry, particularly pH.  However, the fish data, in conjunction with that of other biotic components of the community, may help to refine explanations of the observed relationships.  Interestingly, fish richness in AEAP lakes is significantly positively correlated to pH (Figure 2, r = 0.77, p < 0.01), although this relationship is difficult to explain based solely on the effect of pH in that the fish assemblage has been highly engineered by introductions during the past several decades.  The true value of the fish data will be in the relationships the can be identified among zooplankton, phytoplankton and macrophyte assemblages.  However, the information contained in the fish data base can provide information on several other characteristics of fish assemblages including changes caused by the introduction of exotic species and the fate of native species, movement among individual fish, growth rates of fish based on measurements of tagged individuals, and the abundance of populations in lakes.

fish2A recent manuscript described movement by fish among AEAP study sites (Daniels et al. 2008).  Until recently, many fisheries biologists, particularly fisheries managers, accepted the fact that lakes were isolated from each other.  Our data indicate that a part of each lake population moves among lakes when interconnections occur (Table 5).  This is based on observations of tagged fish caught in new sites and corroborates recent findings elsewhere (Gowan et al. 1994, Gowan and Fausch 1995).

A manuscript describing the impact of an introduction of largemouth bass into Lake Rondaxe and Moss Lake has been completed, but has not yet been submitted.  The effect of the introduction of a large, piscivorous predator on fish assemblages in lakes is well documented (Whittier and Kincaid 1999, Maezono and Miyashita 2003). Our data indicate that the change in fish assemblage structure changes within a few years of the introduction (Figure 3).  The implications for management is that any introduction affects the established assemblage rapidly and suggests that any decision to introduce the exotic species be justified—the decision to do so may lead to a rapid decline in native species and will clearly have a major impact on the structure of the established assemblage.

We have the opportunity to use the length data of tagged fish to follow growth in several species.  These data differ from the typical way of assessing growth in lake fish.  Often, annuli that develop on scales or other bony structures are used to age the fish and back-calculate growth rates (Bagenal and Tesch 1978).  Our database has actual measurements taken over time that allow us to quantify in situ growth in yellow perch, brown bullhead, white sucker, pumpkinseed and rock bass.  These data have not been analyzed fully, but preliminary analyses suggest that: growth rates, particularly among yellow perch are highly variable; large fish do not add length in later years; the winter season is indeed a period of no growth.  Some of these findings corroborate long-held assessments of growth trends in fish; others are unusual.  The database includes growth information on 1029 unique fish from Dart Lake, 1410 from Moss Lake and 946 from Lake Rondaxe.   By species, there is information on 697 brown bullhead, 149 pumpkinseed, 201 rock bass, 964 white sucker and 1374 yellow perch.  This information will be useful in teasing out relationships that are typically not assessed in this way in freshwater studies.

The distribution and abundance of native species and exotic species, as related to elevation, lake size and productivity, was examined using DCA and CCA (ter Braak 1995, ter Braak and Verdonschot 1995).  The DCA and CCA suggest that the species in AEAP sites respond to environmental variables in a predictable way (Figure 4 and Figure 5).  An interesting fish3feature of the DCA is the presence of a cluster of native fishes distinct from a larger cluster largely made up of exotic species.  The DCA assessed abundance.  The results of the analysis suggest that these native fishes are most abundant where exotic forms are absent.  Brook trout, white sucker and creek chub, although present in most lakes, are most abundant in those where they co-occur and where exotic fishes are absent.  The CCA also suggests that these native species may have found refuge from exotic species in smaller, upland lakes where exotic species have not yet been introduced.  These findings again have resource management implications.  It appears that native species do not do well in lakes where exotic species occur and are dominant, and that the refuge lakes are high elevation lakes.  Since these lakes also are affected by changes in water chemistry, the status of native fishes is even more precarious.

In general, the fishery database is a strong adjunct to the databases of the other biotic taxa, but may not provide an unambiguous assessment of change in water chemistry characteristics.  On the other hand, it contains much useful data on the life history and ecology of the fishes found these lakes and can provide valuable guidance to managers and researchers. 

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Adirondack Region National Atmospheric Deposition Program (NADP) Sites

Bennett Bridge.  Over the years, NY52 has recorded some of the highest sulfate (SO4) and nitrate (NO3) deposition amounts in the US and some of the lowest pH values.  Since the Clean Air Act Amendments of 1990, the situation has improved somewhat. Note in the seasonal pH graph, summer usually has the lowest pH (i.e. it is most acid in summer.)  This is presumably due to the more southerly trajectory in summer bringing air from the Ohio Valley region of the country instead of Canada. 

The acidity and concentrations of sulfates and nitrates at Bennett Bridge are amongst the highest in the US, due to Wind trajectories that carry a high percentage of storm systems to the NE US.  Because Bennett Bridge is just upwind of the mountains, which cause rain due their uplift, a large proportion of pollutants are deposited at the site, prior to further transport into New England.  For example, Bennett Bridge shows the highest pollutant values of all sites in the Adirondacks.  The maps below from the NADP 2005 Annual Report show this.  (Maps are taken from  In fact, for many years of the study Bennett Bridge was the highest site in both concentration and deposition of nitrates in the US (e.g. 1997, 1998, 2000, 2001, 2002, 2003).  Thus, we hope that we can get continued funding to keep the site going.

The results from the NADP/NTN site at Bennett Bridge have shown that there have been marked changes in wet deposition chemistry upwind of the Adirondack Mountains of New York.  There have been declines in acidifying components as shown by decreases in sulfate and nitrate, though sulfate has declined much more than nitrate.  These declines have resulted in declines in precipitation acidity (decreases in H+ concentration).  This decline in acidity has, however, been affected by the decline in solutes that are more alkaline, for example, Ca, Mg and Na concentrations.

Small amounts of rainfall tend to be more acid, presumably because the early precipitation takes out more pollutants than the later rainfall when air concentrations are diminished.  When pH is plotted against nitrates or sulfates, the sulfate values are less dispersed, most likely because most of the acidity in the Eastern US is due to sulfates. 
Streamline analysis of air within individual storms has shown that the amount of sulfate and nitrate depends on where the air passes before it is removed by rain at Bennett Bridge.  Highest sulfates tend to come by way of the Ohio Valley and nitrates come from large cities.  Summer trajectories come from farther south than the other seasons causing greater acidity in summer.  Future studies would look at many more examples and use trajectory rather than streamline analysis.

Huntington Forest. The results from the NADP/NTN site at the Huntington Forest has shown that there has been marked changes in the chemistry of wet deposition in the central Adirondack Mountains of New York.  There have been significant declines in acidifying components as shown by decreases in sulfate and nitrate.  These declines have resulted in declines in precipitation acidity (decreases in H+ concentration).  This decline in acidity has, however, been affected by the decline in solutes that are linked with decreasing acidity as shown by the decrease in calcium concentrations.

As aquatic and terrestrial ecosystems in the Adirondack region recover from acidification, it is critical to have accurate measurements in changes of precipitation chemistry.  In addition, at the Huntington Forest, future studies have the potential to evaluate linkages with mercury deposition and changing climatic regimes.  These linkages can be evaluated at the Huntington Forest website  (  In addition to the NADP/NTN measurements, the Huntington Forest is measuring dry deposition (CASTNET) and wet-only mercury deposition (MDN).  The site also has real-time data acquisition ( to evaluate ecosystem and watershed responses. This information also can be integrated into an evaluation of ecosystem health in the region.

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The Watershed Integrated Nitrogen Cycling Study

This study focused on obtaining data on watershed variables including hydrology, vegetation, soil characteristics and land-use history, the variables considered most likely to be related to differential responses of individual watersheds to nitrogen inputs, in the region of New York where nitrogen deposition levels are high and watersheds are most sensitive to acidic deposition.  Click here to be re-directed to a description of this study.

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Brooktrout Lake Special Study

Brooktrout Lake is a relatively small (30-hectare), high elevation (600+m) water located in southwest Hamilton County and one of the 30 study sites selected by the AEAP for investigation in 1994.  This lake represents a major category (thin till, low dissolved organic carbon, drainage waters) of Adirondack water resources that have been severely impacted by acid deposition during the past several decades.  In particular, these impacted waters gradually have lost the sport fish resource that once was widespread and renowned in major areas within the Adirondack region.  The decline of the sport fish resource in Brooktrout Lake was documented by the New York State Department of Environmental Conservation (NYSDEC) during the period from 1950 through 1984.  The full extent of the fisheries resource decline in Brooktrout Lake was the discovery, and realization, that the Lake was “fishless” during a 1984 survey. 

The ALTMP and the AEAP documented significant water quality improvements in Brooktrout Lake during the past two decades.  These improvements in water chemistry and biota suggested that the Lake currently was experiencing partial ‘recovery’ from the long-term effects of acid deposition.  The extent of the ‘positive’ water quality changes observed in the mid-summer data collected at Brooktrout Lake for an extended period of time prompted a major revision of water quality sampling at the Lake and the development of a proposal to re-stock the Lake with brook trout.  Click here to be re-directed to a description of the Brooktrout Lake Special Study.

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moss lakeMoss Lake Atmospheric Deposition Station

The Moss Lake Atmospheric Deposition Station is located in the Town of Webb, Herkimer County, within the watershed of Moss Lake (one of the 30 original AEAP study sites).  The Station was installed in 1988 as part of a cooperative study involving the Adirondack Lakes Survey Corporation (ALSC) and the Massachusetts Institute of Technology (MIT).  Information collected at the station on a regular basis through 1995 included the amount of precipitation (rain and snow) and wetfall samples for chemistry analysis.  The Division of Water, New York State Department of Environmental Conservation, began operation of the Moss Lake Station during the fall of 1995, in conjunction with the AEAP, and continued to operate the Station through 2005.  Information collected at the station on a regular basis since 1995 includes wetfall and bulk precipitation samples for chemical analysis, the amount of precipitation, either rain or snow, recorded at 5-minute intervals, the depth and water content of the winter snowpack, and ambient temperature. 

Data collected at the Moss Lake Station was essential for the two major acid deposition research projects being conducted in the Adirondacks, including the AEAP and the Adirondack Long-Term Monitoring Program (ALTM).  The focal area of both research projects in the Adirondack Mountain region was the southwest quadrant of the Adirondack Park.  The Moss Lake Station is the only deposition facility located directly within the southwest quadrant of the Adirondack Park, which is very important and has distinct advantages since it provides ‘real-time’ values of contaminant deposition and, over the longer term, provides continuous data that evaluates the effectiveness of the 1990 Clean Air Act Amendments and emissions reduction that ultimately impacts a large number of lakes and ponds. 
During July 2003, the Moss Lake Station was added to the National Atmospheric Deposition Program (NADP) network.  Concurrent to becoming part of the NADP, the station site and equipment were refurbished to meet NADP standards and criteria.
Click here to be re-directed to a description of the Moss Lake Atmospheric Deposition Station.

Program Investigators and Personnel

Individuals involved in the AEAP include Rensselaer Polytechnic Institute personnel as well as a number of investigators at other universities, organizations and state institutions.


Rensselaer Polytechnic Institute:

Dr. Sandra Nierzwicki-Bauer:  Co-Principal Investigator, Program Administrator; participant in microbiology studies.
Dr. Charles Boylen:  Co-Principal Investigator; participant in macrophyte, microbiology and watershed studies. 
Mr. Lawrence Eichler:  Research Scientist, design and implementation of macrophyte studies; participant in mid-summer chemistry and biota sampling of study sites.
Mr. David Winkler:  Director, Keck Water Quality Laboratory; provides analytical services for the Aquatic Biota Study; participant in aquatic biota and watershed studies.
Dr. James Harrison :  Post Doctoral Research Associate; database validation; participant in fisheries and aquatic biota field programs; design and implementation of the Brooktrout Lake Fish Restoration Program hydroacoustic studies.


New York State Department of Environmental Conservation:

Dr. James Sutherland:  Collaborative Co-Principal Investigator; Field Program Coordinator for the Aquatic Biota Study; participation in all aspects of aquatic biota and watershed field programs; coordinates work among Program cooperators including RPI, NYSDEC, NYS Museum, USGS via subcontracts with NHT.
Mr. Robert Bombard:  Assistant Research Scientist; participant in mid-summer chemistry and biota sampling of ponded waters, fisheries and watershed studies; responsible for aquatic biota sample inventory; operation and maintenance of Moss Lake Atmospheric Deposition Station.


US Geological Survey:

Dr. Gregory Lawrence:  Collaborative Co-Principal Investigator; Field Program Coordinator for Watershed Nitrogen Cycling Study; coordinate soil chemistry and runoff studies; GIS and database analysis.


New York State Museum:

Dr. Robert Daniels:   Research Scientist; Design and implementation of fisheries surveys and research; directs fisheries data analysis.


University of Maryland:

Dr. Bahram Momen:  Responsible for data analysis and experimental design; participant in watershed studies; primary responsibility for forestry studies.


Institute of Ecosystem Studies:

Dr. William Shaw:  Zooplankton enumeration and data analysis.


Philadelphia Academy of Science:

Dr. Donald Charles:  Phytoplankton enumeration and data analysis.
Mr. Frank Acker:  Phytoplankton enumeration and data analysis.


The State University of New York – College of Environmental Science and Forestry:

Dr. Myron Mitchell:  Atmospheric deposition and forest ecology; operation, maintenance and data analysis associated with NADP site at Huntington Forest.


The State University of New York at Oswego:

Dr. Alfred Stamm:  Atmospheric deposition; operation, maintenance and data analysis associated with the NADP site at Bennett Bridge.


Literature Cited

Bagenal, T.B. and F.W. Tesch.  1978.  Age and growth.  Pages  101-130. In:  Methods for Assessment of Fish Production in Fresh Waters.  Edited by T.B. Bagenal. IBP Handbook No.  3.   Third Edition.  Blackwell Scientific Publications.  Oxford, England.

Daniels, R.A., R. S. Morse, R. T. Bombard, J. W. Sutherland, and C. W. Boylen.  2008.  Fish movement among lakes: Are lakes isolated? Northeastern Naturalist 15: 577-588.

Gowan, C., M.  K. Young, K. D. Fausch and S.C. Riley.  1994.  Restricted movement in resident stream salmonids: A paradigm lost? Canadian Journal of Fisheries and Aquatic Science 51:2626 -2637.

Gowan, C. and K.D. Fausch.  1995.  Mobile brook trout in two high-elevation Colorado streams: Re-evaluating the concept of restricted movement.  Canadian Journal of Fisheries and Aquatic Sciences 53:1370-1481.

Maezono, Y. and T. Miyashita.  2003.  Community-level impacts induced by introduced largemouth bass and bluegill in farm ponds in Japan.  Biological  Conservation  109: 111-121.

Nierzwicki-Bauer, S. A., C. W. Boylen, L. W. Eichler, J. P. Harrison, D. A. Winkler, D. Charles, F. Acker, R. Daniels, G. B. Lawrence, B. Momen, W. Shaw, and J. W. Sutherland.  Adirondack Effects Assessment Program.  FINAL REPORT.  Summary of Aquatic Biota and Watershed Integrated Nitrogen Cycling Studies.  Submitted to the US Environmental Protection Agency, Corvallis, Washington.  April 2008.  15 Chapters, 522 pp.

Momen, B., G. B. Lawrence, S. A. Nierzwicki-Bauer, J. W. Sutherland, L. W. Eichler, J. P. Harrison, and C. W. Boylen.  2006. Trends in Summer Chemistry Linked to Productivity in Lakes Recovering from Acid Deposition in the Adirondack Region of New York. Ecosystems (2006) 9: 1306–13.

Newton, R. M. and C. T. Driscoll.  1990. Classification of ALSC lakes.  Pages 2-70 in J. P. Baker et al. (eds), Adirondack Lakes survey:  an interpretive analysis of fish communities and water chemistry, 1984-87.  Adirondack Lakes Survey Corporation, Ray Brook, NY.

Rensselaer Polytechnic Institute.  1994.  Adirondack effects assessment program, quality assurance (qa/qc) project plan.  Aquatic biota component.  Prepared for US EPA Contract# 68D20171.  Rensselaer Polytechnic Institute, Troy, NY.

Taggett, L.J., J.D. Madsen and C.W. Boylen.  1990.  Annotated bibliography for species richness for submersed aquatic plants in worldwide waterways.  Rensselaer Fresh Water Institute Report #90-0, Rensselaer Polytechnic Institute, Troy, NY.  23 pp. 

Whittier, T.R. and T.M. Kincaid.  1999.  Introduced fish in northeastern USA lakes: Regional extent, dominance, and effect on native species richness.  Transactions of the American  Fisheries  Society  128:769-783.







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