AquaEcology offers a broad spectrum of services for all kinds of water types, such as ponds, lakes, becks, rivers, coastal waters and the open sea. These services are based on many years of expe­rience in research and project work and com­prise com­prehen­sive anal­yses of various para­meters and resto­ration mea­sures for bathing wa­ters and lakes as well as web-based data man­age­ment and pro­gram­ming.

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Analysis of waters

Biological, chemical and physical parameters in the aquatic ecosystem

AquaEcology has got a broad range of parameters for exhaustive investigation of waters: For assessment tools, biological components play an important role. We offer analyses of plankton

as well as of benthic organisms such as
and of
This work in­cludes quan­tita­tive and dif­feren­tiated (down to the spe­cies lev­el) deter­mina­tion of the whole spec­trum of aquat­ic organ­isms and all res­pective qual­ity assur­ance mea­sures. On demand, also other groups (e.g. in­sects, birds) living around aquat­ic habi­tats (river­banks, flood­plains) can be ana­lysed.

By chem­ical anal­ysis, eco­logi­cally rele­vant in­or­ganic and or­ganic sub­stances are deter­mined with high accu­racy. Dif­ferent ana­lytical de­vices and meth­ods are employed, such as Auto­Analyzer, high-tempera­ture cata­lytic com­bustion systems as well as gas (GC) and high-pressure liq­uid chroma­tog­raphy (HPLC).
Physi­cal and physico-chemi­cal param­eters such as temper­ature, salin­ity, oxy­gen content, pH, fluores­cence are ana­lysed with spe­cial in-situ probes and ex­ternal instru­ments.

Concept, sampling, measurement and evaluation

On the basis of many years of ex­perience and of pub­lished sur­vey strat­egies, AquaEcology offers cost-ef­fec­tive con­cepts and alter­natives for measure­ments, ac­cording to the re­spec­tive re­search ob­jec­tive. This in­cludes land-based sam­plings as well as re­search cruises or meso­cosm ex­peri­ments. Prog­nostic models help to under­stand develop­ments and pro­cesses within the eco­system. A se­lected choice of re­spec­tive ana­lyt­ical tech­niques is offered. Eval­uation and graphi­cal anal­ysis fol­low sta­tistic stan­dard proce­dures in the required com­plexity.

AquaEcology works in accor­dance with cur­rent na­tion­al and in­ter­nation­al stan­dards (DIN, CEN) and pro­cedures, and pro­vides the cus­tomer with all neces­sary in­forma­tion on the used methods and on the qua­lity assur­ance measures for the ana­lyti­cal sys­tems. All rele­vant activi­ties, from sam­pling and measure­ment to scien­tific eval­uation, are car­ried out by quali­fied per­sonnel from AquaEcology.

Flow Cytometry

The Flow Cytometry is an analytical method, which is widely used in the medical field and also increasingly being adapted to the biological field. With the Flow Cytometry, single cells such as bacteria, yeast, algae and protozoa can be analysed at high sampling rates in liquid media.

During the analytical process, the cells will pass high-energy light beams with different wave lengths (laser). According to the cell size and granularity, the light will be differently scattered and recorded by the detector.

Moreover, important information can be obtained from existing autofluorescence or from cell compartments such as nucleic acids, lipids et al., stained with specific fluorescent dyes.

AquaEcology is employing the most recent versions of the Flow Cytometry devices and is working only with highly-qualified personnel - also directly at the sampling location if required. Through this, the high-precision results can instantly be used as a basis for decision-making with respect to possible measures and actions.

Flow Cytometry can be applied in the fields of quality assurance and monitoring, research and assessment as well as in the process optimisation. For many applications, this analytical method is much faster, more cost-effective and more precise than the commonly established procedures.

In detail, the Flow Cytometry is offering the following analytical applications:
  • Determination of the total number of individuals
  • Size class analysis
  • Detection of different taxonomic phytoplankton groups (pigment fluorescence)
  • Distinction of active and inactive cells applying specific dyes
  • Analysis of toxic algae and pathogenic organisms using specific fluorescent dyes
  • Calculation of biomass recording DNA amount or autofluorescence
  • Specific detection of pathogens using fluorescent antibodies

Quality assurance and monitoring

For many compartments of the aquatic environment, fast and precise analyses of organisms such as phytoplankton, bacteria and pathogens are required. These requests can easily be met by the Flow Cytometry for a broad variety of parameters - by yielding quick and highly-precise measurements.
  • Treatment of ballast water
    • Compliance with the IMO guidelines
    • Certification
    • Function and effectivity check

  • Surveillance of bathing waters
    • Compliance with the EU guideline for bathing waters
    • Toxic cyanobacteria (blue algae)
    • Hygiene parameters

  • Koi ponds / swimming ponds / aquaria
    • Toxic cyanobacteria (blue algae)
    • Hygiene parameters
    • Pathogenic organisms

  • Environmental monitoring
    • Surveillance
    • Picoplankton / Nanoplankton
    • Toxic algae blooms

  • Analyses of drinking water and milk
    • Hygienic surveillance
    • Microbial counts
    • Pathogens

Research and assessment

Via particle sizes, staining techniques and fluorescent markers, the Flow Cytometry offers various possibilities to analyse organism groups as well as organic molecules such as lipids. Consequently, the method can be well employed in the ecosystemic basic research.

Especially with regard to the numerous national and international marine assessment systems, a lot of interesting applications for the Flow Cytometry are existing.
  • Ecosystem research
    • Abundance and distribution of picoplankton and nanoplankton
    • Biomass estimates via DNA analyses
    • Impact of physical environmental changes
    • Acidification of aquatic systems

  • EU Water Framework Directive
    • Shifts in taxonomic and functional groups
    • Analyses of processes and turnover in the food web

  • EU Marine Strategy Framework Directive
    • Shifts in taxonomic and functional groups
    • Questions of biodiversity
    • Impact of offshore wind farms

Process optimisation

Due to the capability of fast and precisely counting microorganisms, also very specifically, the Flow Cytometry is very suitable for process analyses in various applied systems.

  • Biogas plants
    • Monitoring and surveillance
    • Activity and effectivity check

  • Sewage plants
    • Monitoring and surveillance
    • Activity and effectivity check

  • Production of algal biomass
    • Monitoring and surveillance
    • Activity and effectivity check

Please, just contact us and tell us about your requirements and problems. We will be glad to set up an individual concept for sampling and analysis for you.

DNA Analyses

Parallel to the development and mass usage of the polymerase chain reaction (PCR) within the DNA analysis, costs have dropped and at the same time, the scope of potential and specific applications has broadened. Consequently, it is possible to determine gene sequences being very specific for certain organisms and thus, to acquire additional taxonomic data and information on aquatic organisms such as plankton, macrozoobenthos, and fishes.

In a close co-operation with a qualified scientific partner AquaEcology now offers a comprehensive and detailed determination of aquatic organisms using DNA analyses. In particular, we recommend three application methods: DNA Barcoding Metabarcoding eDNA Analyses All three methods allow a fast and reliable determination of organisms and organism groups in water.

They are described as follows:

DNA Barcoding

DNA barcoding is the identification of organisms based on the Sanger sequencing of a defined gene fragment ('barcoding fragment'). For this purpose, the DNA will be isolated and the barcoding fragment multiplied by PCR. The sequenced PCR product will be compared to sequences from a reference database. If the match has a probability > 98 % then the sampled species can be assigned to a known species of the database.


DNA metabarcoding allows the genetic analysis of bulk samples representing a mix of different organisms. This includes water samples of plankton and macrozoobenthos. The sample is homogenized and analyzed using high-throughput parallel sequencing. Sequences are then computer-processed to obtain the species composition of the mixed sample.

eDNA Analyses

eDNA analysis is a new tool to determine species by non-invasive sampling. This procedure is useful for rare or endagered species as well as for species in proteced areas. The term eDNA refers to all traces of genetic material left by organisms in their own environment through the release of faeces, urine, gametes, mucus, etc. A broad range of molecular methods (qPCR, Sanger and High Throughput Sequencing) can be used to recover and analyze this eDNA, and, for instance, reveal the composition of species in a water sample even if the targeted species are not present at the sampling site any longer.

Please, just contact us. We will provide you with an individual concept for sampling and analysis according to your taxonomic requests.

Assessment of aquatic impacts

General ecosystem analysis

Based on re­cent data from sur­veys, on histor­ical data and on data from eco­system model­ling, AquaEcology com­piles func­tional anal­yses of aquat­ic sys­tems. These anal­yses are manda­tory for the detec­tion of ef­fects of per­tur­ba­tions with­in the high­ly com­plex food web and for the re­spec­tive assess­ment.
In ex­peri­mental se­ries, eco­toxi­colog­ical im­pacts of chemi­cal com­pounds on dif­ferent aquat­ic organ­isms are in­vesti­gated and eval­uated; these investigation are also an integral part of the cumulative effects analyses as required by the Marine Strategy Framework Directive (MSFD).

Specific and international procedures

In cases of ur­gent pro­blems, object-spe­cific assess­ment and inter­nation­ally estab­lished pro­cedures are offered. The former com­prises a small selec­tion of param­eters, while the lat­ter are speci­fied ac­cording to inter­nation­al guide­lines (European Water Frame­work Direc­tive - WFD, OSPAR guide­lines). Within this frame, also ex­ter­nal data can be in­cluded and be eval­uated sepa­rately.

Environmental impact statements

In the frame of environmental impact analyses, bio­log­ical or hydro­chemi­cal expert's re­ports for re­placement activi­ties, for new construc­tions or for changes in waste­water dis­charges are com­piled. Of course, the whole pro­cess will be pro­fession­ally accom­panied by AquaEcology.

Consulting and projecting

AquaEcology offers consult­ing and manage­ment for big­ger pro­jects. This in­cludes the prep­ara­tion of a consult­ing con­cept, the reali­sa­tion of the planning and or­gani­sation of the logistics as well as con­ducting all the proce­dures in­clu­sive of the neces­sary measure­ments. Partic­ular appli­cation ranges are the resto­ration of waters, scien­tific re­search proj­ects and meso­cosm ex­peri­ments as well as ballast wa­ter treat­ment and aqua­culture manage­ment.

Projecting of restoration and protection measures

Many natu­ral wa­ters lost their orig­inal eco­logi­cal balance due to eutro­phi­cation or con­tami­nation with pol­lutants. As a con­sequence, massive algae blooms occur, very often also con­taining harmful and toxic blue-green algae and even leading to kill­ings of micro­organisms, benthic animals and fishes. AquaEcology develops concepts for resto­ration and pro­tection mea­sures, also includ­ing alter­native tech­nical possi­bilities. By con­ducting pilot studies, the ex­pected ef­fects can be test­ed and then be simu­lated by model­ling.

Effect-oriented time and cost schedules for water body restoration

Alter­native con­cepts for water body resto­ration are spe­cifi­cally adapted to the problem and to the type of water body, con­sidering the optimal cost-benefit anal­ysis and the time tar­get. At the same time, col­lat­eral public rela­tion mea­sures in the form of semi­nars, lec­tures, flyers and bro­chures can be con­ducted.

Scientific projects

AquaEcology has a supportive part in inter­disci­plinary and inter­national re­search proj­ects, also within the frame of con­tract re­search. Exten­sive meso­cosm ex­peri­ments can be planned and carried out, in order to trace bio­geo­chemi­cal pro­cesses in dif­ferent water bodies. Ana­lyt­ical con­cepts for test­ing bal­last water ac­cording to IMO guide­lines are prepared and realised. An­other proj­ect field is the moni­toring and optimi­sation of aqua­culture systems.
As col­lat­eral mea­sures in the scien­tific pro­jecting, the insti­tute offers profes­sional teachings in the field of aquat­ic ecol­ogy; this could be done in the form of seminars, work­shops, ex­cursions and prac­tical courses.

Restoration and protection


Based on the elabo­rate con­cept and the planning, AquaEcology puts the mea­sures into prac­tice, also in co-opera­tion with other spe­cial­ists when ap­pro­priate. Ac­cording to the water body type and to the se­veri­ty of the prob­lem, aera­tion with oxy­gen or re­mov­al of sedi­ments is carried out. In order to achieve an in­sol­uble bind­ing or an effec­tive removal of prob­lem sub­stances from the water column or the sedi­ment, certain precipitants or bind­ing agents can be applied. As long-term mea­sures for removal of nu­trients, con­struc­tion of reed bed systems close to the banks are offered.

Analysis, monitoring, evaluation and training

In order to ensure medium and long-term ef­fects of the res­tora­tion and pro­tec­tion mea­sures, they are moni­tored by speci­fied anal­yses and eval­uated in terms of ef­fec­tive­ness. Within this con­text, project-as­signed per­son­nel can be trained for the long-lasting moni­toring and service work. By all this, the mea­sures can be super­vised, from so­lic­iting a quo­ta­tion to the con­comi­tant anal­ysis and the final ac­cep­tance.

Data management und software

Data storage and documentation

All the data from anal­yses and mea­sures as well as ex­ter­nal en­viron­mental data can be stored user-friendly and inter­active­ly in data­bases and be processed for spe­cif­ic re­quests. Anal­yses and as­sess­ments are docu­mented fol­low­ing ac­cred­ited pro­ce­dures. Further­more, AquaEcology of­fers scien­tif­ic sta­tis­ti­cal and graphi­cal eval­uation of ex­isting data sets.

Databases and server hosting

AquaEcology offers the de­velop­ment of user-friendly, web based data­base systems such as taxo­nomic image data­bases for all kinds of organism groups. The under­lying system is the new soft­ware biodivDP which is indi­vidu­ally adapted and imple­mented for each appli­cation. A prominent example is the inter­nation­ally es­tab­lished taxo­nomic phyto­plankton data­base Plankton*Net, which ef­fec­tively con­trib­utes to the field of bio­diver­sity re­search. The de­vel­op­ment and im­ple­men­tation of this data­base was funded by fi­nan­cial means from the BIS Bremer­havener Ge­sell­schaft für In­vesti­tions­förderung und Stadt­ent­wick­lung mbH as well as from the Eu­ro­pe­an Union.

For an optimisation of the data management, AquaEcology has got fur­ther ser­vices in its ten­der, such as serv­er hosting for data­bases, data mainte­nance and the devel­op­ment of spe­cial tools for ad­minis­tra­tion, transfer, pre­sen­tation and eval­uation of data.

Development of software

AquaEcology develops various software tools for the appli­cation in biological scientific information systems and data­bases. This includes the newly devel­oped web-based counting programm OrgaCount, which is cur­rent­ly im­ple­mented for en­ter­ing phyto­plankton, zooplankton and macrozoobenthos counts, but can also be used for any other or­gan­ism group or countable item.

List of Services

In the following, a detailed list­ing of all the ser­vices is given, of­fered by AquaEcology in the field of aquat­ic ecol­ogy:

Phytoplankton (marine, estuarine and fresh water)

  • sampling and sample processing
  • qualitative analysis of species
  • quantitative analysis of abundances
  • biovolume, biomass
  • preparations of diatoms inclusive of species abundances
  • chlorophyll und other photosynthesis pigments
  • primary production
  • data management and evaluation
  • assessment according to the European water framework directive (WFD)

Water samples or net catches are analysed and listed for phyto­plankton of all taxo­nomic groups, using the up­dated nomen­clature. In fixed water samples, the phyto­plankton organ­isms are iden­tified with an in­verted micro­scope and counted on the spe­cies or group level, in order to deter­mine cell density per volume unit (e.g. indi­viduals per litre). For esti­mating the phyto­plankton bio­mass with­in the sam­ples, every species is as­signed to a geo­metric body, whose aver­age dimen­sions are de­rived from a re­presen­tative num­ber of cells for each spe­cies. The bio­volume cal­cu­lated on this ba­sis is then con­verted into car­bon bio­mass.

The chloro­phyll con­cen­tra­tions in the water column are a mea­sure of the ex­isting phyto­plankton bio­mass. Chloro­phyll is deter­mined either by a fluoro­meter - as ac­tive chloro­phyll in living cells with an 1-Hz-fluoro­meter - or after fil­tra­tion and ex­trac­tion by photo­metric detec­tion. Further photo­synthesis pig­ments are quanti­fied by HPLC.

The pri­mary pro­duction is ana­lys­ed using the light-dark oxy­gen meth­od. With ex­isting fa­cili­ties, also radio­active 14C can be used for the deter­mination.

Zooplankton (marine, estuarine and fresh water)

  • sampling and sample processing
  • qualitative analysis of species
  • quantitative analysis of abundances
  • analysis of size classes, biomass
  • respiration
  • data management and evaluation

Water samples or net catches are analysed and listed for zoo­plankton of all taxo­nomic groups, using the up­dated nomen­clature. In fixed water sam­ples, spe­cies and group abun­dances are deter­mined, in order to ob­tain den­sity of in­divid­uals per litre. For cope­pods, dif­ferent devel­opment stages are de­tected. From a rep­resen­tative num­ber of individuals, the size is mea­sured.

Res­pira­tion is deter­mined using the oxy­gen meth­od.

Bacterioplankton / bacteria (marine, estuarine and fresh water)

  • sampling and sample processing
  • quantitative analysis of abundances of morphological groups
  • bacterial production, respiration
  • rapid tests E. coli, coliforms, enterococci
  • data management and evaluation

The num­ber of free and par­ticle-bound bac­teria in the water column is de­tected with an epi­fluo­res­cence micro­scope fol­lowing stain­ing with spe­cial col­ours. Dif­ferent morpho­logical types are re­garded. For esti­mating the car­bon bio­mass, sizes of dif­ferent types are deter­mined and con­verted with fac­tors.

With ex­isting fa­cili­ties, bac­terial pro­duction (build-up of bio­mass) can be mea­sured with radio­labelled sub­strates.

  • design of specific oligonucleotides
  • primer design

Based on 16S rRNA gene se­quences high­ly spe­cif­ic oli­go­nu­cleo­tides can be de­signed. These oli­go­nu­cleo­tides are intended to be used for spe­cif­ic PCR or hy­brid­iza­tion tech­niques like fluo­res­cence in situ hy­brid­iza­tion (FISH) and can be op­ti­mised for dif­fer­ent meth­ods.

Phytobenthos (estuarine and fresh water)

  • sampling and sample processing
  • qualitative analysis of species of all taxonomic groups
  • quantitative analysis of abundances of all taxonomic groups
  • preparations of diatoms inclusive of species abundances
  • data management and evaluation
  • assessment according to European water framework directive (WFD)

Phyto­benthos sam­ples of dif­ferent sub­strate ori­gin are ana­lys­ed and listed for spe­cies of all taxo­nomic groups (e.g. cyano­bacteria, diatoms, green algae and others), using the up­dated nomen­clature. If pos­sible, quanti­fication will be done on the spe­cies lev­el, other­wise higher taxo­nomical lev­els and spe­cific groups will be ana­lysed.

Macrophytes (estuarine and fresh water)

  • field survey, sampling and sample processing
  • qualitative analysis of species
  • quantitative analysis of degree of coverage
  • data management and evaluation
  • assessment according to European water framework directive (WFD)

The macro­phytes in the water as well as in the near bank areas are ana­lys­ed and listed, using the up­dated nomen­clature. Further­more, abun­dances and de­grees of cov­er­age are deter­mined. Groups that are dif­fi­cult to deter­mine in the field, are re­worked in the labo­ratory.

Macrozoobenthos (marine, estuarine and fresh water)

  • sampling and sample processing
  • qualitative analysis of species (grabber, dredge system)
  • quantitative analysis of abundances (grabber, dredge system)
  • analysis of dry weight, biomass
  • data management and evaluation
  • assessment according to European water framework directive (WFD)

Sediment samples or dredge catches are analysed for spe­cies and abun­dances of macro­zoo­benthos ac­cording to the up­dated nomen­clature.

Fishes (marine, estuarine and fresh water)

  • electrofishing and other methods
  • qualitative analysis of species
  • quantitative analysis of abundances
  • analysis of size classes
  • age distribution
  • data management and evaluation
  • assessment according to European water framework directive (WFD)

By using modern and gentle methods (e.g. electro­fishing), spe­cies and abun­dances of fishes are deter­mined in the aquat­ic sys­tem. Further­more, sizes of the in­divid­uals and age distri­bution can be ana­lys­ed within the com­munity.

Dissolved chemical substances (marine, estuarine and fresh water)

  • sampling and sample processing
  • nutrients (ammonium, nitrate, nitrite, phosphate, silicate)
  • carbohydrates, amino acids
  • oxygen
  • heavy metals
  • organic pollutants (on request)

In fil­tered water sam­ples, the dis­solved nutrients are ana­lys­ed by con­tinuous-flow anal­ysis (CFA) with photo­metric de­tec­tion (AA3 sys­tems, Seal GmbH). For to­tal dis­solved phos­phorus (TDP) and nitro­gen (TDN), the CFA is pre­ceded by diges­tion with per­oxo­di­sulphate in an auto­clave. To­tal or­ganic car­bon (TOC) is mea­sured with high-temper­ature cata­lytic oxi­dation (HTCO) de­vices, while carbo­hydrates and amino acids are ana­lys­ed with HPLC sys­tems. For the quanti­fication of oxy­gen, the Winkler meth­od with a Metrohm ti­tration stand is used. The heavy metals are deter­mined with AAS.

Particulate chemical substances (marine, estuarine and fresh water)

  • sampling and sample processing
  • PC, PN, PP
  • pigments
  • heavy metals and organic pollutants (on request)

Particulate carbon (PC) and nitrogen (PN) are direc­tly mea­sured from fil­ters by using HTCO de­vices. Partic­ulate phos­phorus (PP) is photo­metri­cally ana­lys­ed with AA3 after di­gestion with per­oxide and sulphuric acid. Pig­ments are ex­tracted from fil­ters and deter­mined by HPLC.

Hydrography (marine, estuarine and fresh water)

  • field survey, sampling
  • temperature
  • salinity, conductivity
  • density
  • redox potential
  • turbidity, fluorescence
  • light irradiation
  • pH value

During field surveys on research vessels or in meso­cosm ex­peri­ments, vari­ous physi­cal and physico-chemi­cal para­meters are re­corded in-situ with auto­matic probe sys­tems.

Environmental impact analysis (marine, estuarine and fresh water)

For ecological assessments being a basis for en­viron­mental impact anal­ysis, ex­pert's re­ports in the hydro­chemical and in the hydro­bio­logical field are of­fered for var­ious para­meters:

  • hydrochemical expert's reports - water as subject of protection
    • water quality: salinity, oxygen, nutrients, particulate matter, pollutants
    • pollutants in sediments: heavy metals, PCBs, HCHs, tin organic compounds
  • hydrobiological expert's reports
    • fauna as subject of protection: zooplankton, macrozoobenthos, fishes
    • flora as subject of protection: phytoplankton, phytobenthos, macrophytes
    • European water framework directive (WFD)

Water treatment

  • concepts and expert's reports for the restoration of natural waters
  • tests of ballast water treatment systems according to IMO guidelines
  • management of aquacultures


  • national and international research projects
  • contract research


  • academic teaching (lectures, workshops, practical courses)
  • popular science (presentations, excursions)
  • further education (seminars, workshops)

Data analysis

  • statistical analysis
  • graphical analysis
  • evaluation

Data bases

  • development of web based databases derived from the software biodivDP
  • implementation, maintenance, quality assurance
  • server hosting
  • development of specific tools