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Substratum-Associated Microbiota

October 2010
Water Environment Research 82(10):1903-1944

October 2010
82(10):1903-1944

DOI:10.2175/106143010X12756668802094

Authors:

Antonia Liess

Halmstad University

Steven N. Francoeur

Eastern Michigan University

A review of literature on substratrumassociated microbiotia from 2013 covers topics on benthic algae, bacteria and viruses from a range of aquatic environments, but focuses on freshwater ecosystems. Advances in laboratory, field, and assessment methods are highlighted as are updates in taxonomy and systematics. Aspects of water quality, waste-water treatment, biofuels, nutrient cycling, food-web interactions, land use changes, and environmental challenges such as climate change, pollutants, and impacts of medical substances are presented. our understanding of the ecology, taxonomy and assessment of substratum-associated microbiota. In response to increased pressures from anthropogenic stressors and climate change on aquatic environments, researchers are re-evaluating current knowledge and approaches to research, biomonitoring and assessment. In this review of the 2013 literature, advances in laboratory, field, and assessment methods are highlighted as are updates in taxonomy and systematics. A literature review of similar topics was completed in 2013 (Furey and Liess, 2013).

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Substratum-Associated Microbiota

Antonia Liess1 and Steven N. Francoeur2*

ABSTRACT: A review of the literature published in

2009 on topics relating to on the subject of ecology of

substratum-associated microbiota (algae, bacteria, fungi

and viruses). We also highlighted some of the new

methods that can be applied to the study of substratum-

associated microbiota and included newly described

taxa.

KEYWORDS: algae, bacteria, fungi, periphyton,

biofilm.

doi: 10.2175/106143010X12756668802094

Methods

Algae. Advances were made in the measurement

of biomass and growth, primary production, community

—————————

1 Umeå University, Department of Ecology and Environmental

Science, Umeå, Sweden

2* Center for Aquatic Microbial Ecology, Biology Department, 316

Mark Jefferson Hall, Eastern Michigan University, Ypsilanti,

Michigan USA, steve.francoeur@emich.edu

This work was supported by Lake Ecosystem Response to

Environmental Change (LEREC) project funded by the Swedish

Research Council for Environment, Agriculture and Spatial

Planning (FORMAS), and the EMU Center for Aquatic Microbial

Ecology.

composition of benthic algae as well as in the development

of benthic algal specific molecular tools. A new remote

sensing technique allows non-destructive, inexpensive and

quantitative measurements of chlorophyll in situ, which can

be applied to the study of intertidal and freshwater benthic

habitats (Murphy et al., 2009). The technique of in vivo

growth fluorometry, well suited for use on benthic

microalgae, is based on the sensitive detection of in vivo

chlorophyll a fluorescence and monitors its increase over

time as an indicator for growth (Gustavs et al., 2009).

Group-specific primary production can be estimated based

on stable-isotope labeling of phospholipid-derived fatty

acids and will be applicable to benthic algal mats (Dijkman

et al., 2009). A high-frequency echosounder was used to

detect and characterize benthic filamentous algal stands on

rocky substrata (Depew et al., 2009). Molecular tools for

assessment of taxonomic composition of a benthic algal

community were tested and results suggest that genus level

identification might be attainable (Manoylov et al., 2009).

Ten polymorphic microsatellite markers were developed

and tested for the benthic freshwater diatom Sellaphora

(Evans et al., 2009). Lastly, a new cell primo-culture

method was developed for the benthic diatom community

isolated from biofilm sampled in rivers (Debenest et al.,

2009).

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Bacteria. Boehm et al. (2009) developed a

standardized protocol for extracting fecal indicator bacteria

from beach sand. Disruption and storage unpredictability

altered extracellular enzyme activities of aquatic biofilms

(Smucker et al., 2009). Analysis of stable hydrogen

isotopes was a useful adjunct to analysis of stable carbon

isotopes for analysis of bacterially-supported aquatic food

webs (Deines et al., 2009). Weber et al. (2009) developed

a new multivariate technique for analysis of Biolog plates.

A dilution-based method was developed for analysis of

sediment-associated viruses (Dell’Anno et al., 2009).

Spore-forming strains of Bacillus in lake sediments were

used to infer paleoclimate and nitrogen conditions (Suslova

et al., 2009). Different DNA extraction protocols affected

the number and intensity bands in DGGE community finger

printing analyses (Tang et al., 2009). Real-time PCR assays

for enumerating acetogens (Xu et al., 2009a) and genotype

bacteriophages (Haramoto et al., 2009) were developed. A

PCR-DGGE assay was developed for detection and

diversity analysis of neutrophilic iron oxidizers (Wang et

al., 2009a). Nested automated ribosomal intergenic spacer

analyses (ARISA) proved to be a useful tool for bacterial

community structure analysis (Lear and Lewis 2009b).

Stankiewicz et al. (2009) developed a new technique for

labeling and recovering biofilm bacterial RNA. Culture-

independent estimates of sulfate-reducing bacterial

abundance were superior to culture-based methods for

detecting ecological patterns in sediments (Ramamoorthy et

al., 2009). Lin et al. (2009) developed a RFLP-based

technique for analysis of magnetotactic bacteria in lake

sediments. Accounting for spatial variability at different

spatial scales improved the ability of a field monitoring

program to detect the effect of pesticide on lotic microbial

communities (Dorigo et al., 2009). Briand (2009) reviewed

methods used to prevent biofouling by microbes.

Fungi. Incubation of natural foam recovered

more hyphomycete taxa than incubation of artificial foam

or leaves (Pinto et al., 2009). Ergosterol and ATP content

of leaf litter were positively correlated during early (<40d)

colonization, but were uncorrelated after this time (Abelho,

2009). A calcofluor white-based protocol was developed

for enumerating planktonic chytrids (Rasconi et al., 2009);

this protocol may be useful for substratum-associated

microbial communities.

Other. Confocal laser scanning microscopy may

provide an improved way to enumerate viruses (Luef et al.,

2009). Scanning transmission X-ray microscopy can be

used to examine microscale elemental distributions in

aquatic biofilms (Hitchcock et al., 2009).

Taxonomy and Systematics

Algae. Some taxonomic reorganization, due to

the use of light and scanning electron microscopy and

molecular phylogenetic analyzes was done. New

information on a diatom species Fragilaria hungarica from

Lake Balaton, Hungary, using light and scanning electron

microscopy, supported its transfer to the genus Staurosira

Ehrenberg and a new name Staurosira grigorszkvi nom.

nov. was proposed (Acs et al., 2009). A new benthic

freshwater diatom, Geissleria gereckei sp. nov., was

identified from light and scanning electron micrographs

(Cantonati and Lange-Bertalot, 2009). Molecular

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phylogenetic analysis revealed that the green algae

Uronema curvatum was closely related to the Ulvophycean

order Cladophorales instead of Chlorophyceae.

Additionally, the epiphytic Urospora microscopica from

Norway was transferred to the cladophoralean genus

Chaetomorpha as C. norvegica nom. nov. (Leliaert et al.,

2009). The marine endophyte Phaeostroma endophyticum

was moved into the genus Chukchia and became Chukchia

endophytica (Wilce et al., 2009).

Bacteria. New Gram-negative bacteria were

isolated from Korean lake (An et al., 2009) and stream (Xu

et al., 2009b) sediments, and from a Korean tidal flat (Yoon

et al., 2009b) and saltern (Yoon et al. 2009a). Novel Gram-

negative were isolated from a eutrophic Chinese lake (Qu

et al., 2009a; Qu et al., 2009b) and an alkaline Chinese lake

(Liu et al., 2009). Three new halophilic aerobic bacteria

were isolated from a Chinese salt lake (Chen et al., 2009a;

Chen et al., 2009b; Chen et al., 2009c). Novel anaerobic

bacteria were discovered in Tunisian (Hedi et al., 2009) and

North American (Pikuta et al., 2009) lakes. A new purple

non-sulfur bacterium (Boldareva et al., 2009a) and a novel

bacteriochlorophyll-a-containing bacterium (Boldareva et

al., 2009b) were discovered in the sediments of Siberian

soda lakes. New species of iron-reducing bacteria (Zhilina

et al., 2009a; Zhilina et al. 2009b), an anaerobic diazotroph

(Zavarzina et al., 2009), a nitrile-degrading bacterium

(Sorokin et al., 2009) and a facultative anaerobic bacterium

with a wide range of terminal electron acceptors (Baesman

et al., 2009) were also isolated from soda lake sediments.

New sulfate-reducing bacteria were discovered in metal-

contaminated lake sediments (Sass et al., 2009) and an

acid-mine drainage wetland (Lee et al., 2009).

Fungi. A molecular phylogeny of Tricladium did

not support morphological classifications. Several taxa

were shown to be polyphyletic (Campbell et al., 2009).

Culture and molecular analyses suggested a similar pattern

of evolution in both aquatic and marine cyphelloid

basidiomycetes (Yamaguchi et al., 2009). Molecular and

morphological re-examination of several genera in the

Pleosporales indicated that some existing genera are

polyphyletic. A new genus and 5 new species were

described (Zhang et al., 2009a. A molecular and

morphological analysis led to the description of a new

species of Sigmoidea, and the errection of a new genus,

Halosigmoidea, to accommodate marine taxa previously

placed in Sigmoidea (Jones et al., 2009). Mozley-

Standridge et al. (2009) suggested a new monophyletic

order of chytrids. A new genus and several novel species

were described from the Americas (Raja et al., 2009b;

Soares et al., 2009).

Algal Ecology

Spatial distribution. Benthic and epiphytic

community structuring mechanisms were investigated in

springs, streams, rivers, and marine intertidal and costal

habitats. In an ephemeral pristine stream, the composition

of algal assemblages was primarily influenced by the type

of substratum and by the spatial distance from the stream

origin (Vesela, 2009). In the Gangqu River, Shangrila,

China, the spatial distribution of benthic algae in relation to

environmental variables was analyzed to establish baseline

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conditions (Wu et al., 2009b). Abundance and community

structure of epilithic algae in mountain streams of

subtropical Taiwan were studied to examine the effects of

intensive agriculture in mountain streams of the Wuling

area (Yu and Lin, 2009). Patterns of periphyton

chlorophyll and dry mass along an altitudinal gradient in a

neotropical stream in the Brazilian Atlantic rainforest were

assessed with a cheap and rapid analysis using a hand-held

fluorometer (Moulton et al., 2009). An evaluation of how

benthic algal assemblages remove NO3-N from the water

column of a mountain stream, indicated that increased

assemblage diversity leads to higher rates of community

processes and that algae in some patch types might be

capable of meeting -nitrogen demands via N2-fixation

(Baker et al., 2009). Diatom species distribution and their

pH and conductivity dependence in 15 headwater streams

in the Elbsandsteingebirge region of the Czech Republic

were studied. 307 diatom taxa were observed, including

one species new to science, Chamaepinnularia rexii

(Vesela and Johansen, 2009). The diversity of the genera

Pennate diatoms in the Punjab province of Pakistan, from

different freshwater habitats, was investigated (Tariq-Ali et

al., 2009). The biodiversity patterns of benthic diatom

assemblages in a Mediterranean semiarid stream revealed

that species richness and diversity were correlated with

hydrology and sulfate concentrations, whereas biomass was

associated with variations in temperature, conductivity and

ammonium (Ros et al., 2009).

The distribution of algal epiphytes across

environmental gradients of intertidal elevation, host

canopies and host fronds was examined to identify likely

causes behind the observed patterns in relation to

predictable changes in abiotic factors (Longtin et al., 2009).

The investigation of epiphytic diatom communities on

macroalgae from Iceland coastal waters during July 2005

found that highly branched seaweeds with articulated

thallus surfaces showed a high level of colonization, mainly

by erect and motile diatoms (Totti et al., 2009). The spatial

distribution of epiphytic diatoms on lotic bryophytes

contrasting morphologies in stream ecosystems found that

the morphology of mosses provides a greater level of

protection from disturbance than open and flat liverworts

(Knapp and Lowe, 2009). Epiphytic diatoms on Galaxaura

rugosa in the Fernando de Noronha Archipelago in

Northeast Brazil were investigated and their diversity was

found to be medium to high (Costa et al., 2009). The role

of environmental variables in structuring epiphytic and

epilithic diatom assemblages in springs and streams of the

Dolomiti Bellunesi National Park (south-eastern Alps) were

investigated. Many poorly known, rare, or Red List species

were found in springs, highlighting the important role of

springs as valuable habitats for the conservation of aquatic

biodiversity (Cantonati and Spitale, 2009).

Temporal variation. Temporal, mainly

seasonal, variation of benthic algal community composition

and biomass in dams, lakes and streams was monitored.

Changes in the epipelic algal flora in the Balikli Dam

Reservoir between May and November 2006 showed that

ice, light, rainfall and water temperature were the most

important factors in regulating the growth of epipelic algae

and species composition (Kolayli and Sahin, 2009b).

Monitoring seasonal variation in species composition of the

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benthic algal community of Karagol Lake showed that

Chlorophyta!were dominant in terms of species number and

abundance!and that benthic algal growth was mostly

influenced by water temperature and light (Kolayli and

Sahin, 2009a). Gradually increasing salinity in the Large

Aral Sea during the last few years led to changes of the

benthic algal community, consisting of microphytobenthos,

macrophytes, and microepiphytes (Sapozhnikov et al.,

2009). A survey of annual changes in lake algal abundance

and community composition found that the highest

proportion of true epipelic algae in sediments was reached

in the second clear phase and that they were dominated by

Oscillatoriaceae throughout the entire year (Casco et al.,

2009). Measuring periphyton biomass, potential

production and respiration in a shallow lake during winter

and spring found a high productive capacity of winter

periphyton and resulting high periphytic biomass early in

the season (Liboriussen and Jeppesen, 2009). A study on

seasonal abundance, community composition, and silica

content of diatoms epiphytic on Cladophora glomerata in

the Great Lakes showed that silica content can be a

valuable proxy for diatom epiphyte abundance if the

vitality of the Cladophora substrate is considered (Malkin

et al., 2009). The depth-distribution of epilithic diatoms in

an oligotrophic lake characterized by marked water-level

fluctuations showed that community composition and

diversity depth-distribution features remained relatively

stable throughout the year (Cantonati et al., 2009).

Seasonal and spatial variations in epilithic algal

assemblages in streams in monsoonal Hong Kong were

investigated (Yang et al., 2009). Temporal variation in

substratum-specific rates of N uptake and metabolism and

their contribution at the stream-reach scale were quantified

in situ in microcosms, during spring, summer, and autumn

in three headwater streams in northern Michigan (Hoellein

et al., 2009). Streambed substratum composition

influenced seasonal variability of reach-scale nutrient

uptake by its influence on metabolism and changed the

relative contribution of several substrata to whole-stream

rates through time. Finally, diurnal variation in periphtyon

nutrient uptake was found to be high, especially in open

canopy streams and when nutrient uptake was driven by

autotrophs (Johnson and Tank, 2009).

Benthic productivity. Benthic algae are

important contributors to the primary productivity of

aquatic ecosystems, both in rivers, lakes and marine

ecosystems. Primary production and carbon dioxide

metabolic balance of a lake-rich arctic river floodplain on

the Mackenzie Delta was partitioned into phytoplankton,

epipelon, macrophyte, and epiphyton production. Results

show the large river floodplains are remarkably productive

aquatic ecosystem with a high proportion of benthic

productivity (Squires et al., 2009). By using stable carbon

(delta C-13) and nitrogen (delta N-15) isotopes, it was

found that benthic algae support zooplankton growth

during winter in a shallow, clear subarctic lake (Karlsson

and Sawström, 2009). Whole-lake estimates of carbon flux

through algae and bacteria in benthic and pelagic habitats

of clear-water lakes in subarctic northern Sweden suggest

that productivity in these lakes is largely determined by

benthic autotrophic production and metabolism of

allochthonous organic carbon (Ask et al., 2009). In

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addition, it was found that phytobenthos and phytoplankton

pigment strategies differ which implies divergent responses

to environmental change between the phytobenthos and

phytoplankton in high latitude lakes (Bonilla et al., 2009).

But even at low latitudes benthic production is of

importance. A mass-balanced model of the trophic

dynamics of a newly-impounded south-east Asian

reservoir, Pasak Jolasid, Thailand (monitored from its

creation), showed that benthic algae as well as

phytoplankton were important components of the reservoir

food web (Thapanand et al., 2009). Long-term microcosm

experiments in shallow lakes, investigating competition

between benthic and pelagic microalgae for phosphorus

and light found that benthic algae were always dominant

(Pasternak et al., 2009). A comparison of biomass and

primary productivity of benthic microalgae and planktonic

algae in the Seto Inland Sea, Japan in 2002 found that the

contribution of benthic microalgae to the total biomass was

7% in winter and 2% in summer and that primary

production of benthic microalgae accounted for 2-12% of

the total primary production (Sarker et al., 2009). High

benthic microalgal biomass was also found on Ship Shoal

on the north-central Gulf of Mexico, suggesting that

benthic primary production may contribute to the Ship

Shoal food web and that benthic primary production may

be an important ecosystem component on the other large

shoals found on Louisiana's inner shelf (Grippo et al.,

2009).

Polar Algae and Ice Algae. Five reviews dealt

with abiotic and biotic restrictions that polar benthic

microalgae have to cope with. First, composition,

biogeography and zonation of benthic algae in Arctic and

Antarctic polar regions were reviewed (Wulff et al., 2009).

Zonation or local distribution of polar microalgae was

influenced by physiological, morphological, chemical and

ecological characteristics that determine responses to a

range of environmental factors, including the ability to

resist and survive algal grazing. Second, present

knowledge on how UV radiation affects the physiology of

polar benthic algae was discussed (Karsten et al., 2009).

Third, a summary of polar studies showed that marine

benthic microalgae in polar regions have a striking ability

to photosynthesize and grow under very low light and

temperature conditions, an adaptation which allows benthic

marine algae to make high contributions to high latitude

coastal primary productivity and energy fluxes, exceeding

or equaling the production of primary producers in more

temperate systems (Gomez et al., 2009). Fourth, a review

of drivers of colonization and succession in polar habitats

found that biotic factors, such as grazing, can strongly

affect colonization patterns and also alter competitive

interactions among benthic algae (Campana et al., 2009).

Last, the abiotic environment of polar marine benthic algae

and the differences between Antarctica and the Arctic in

oceanographic and geological characteristics and their

benthic algal communities were discussed (Zacher et al.,

2009).

Ice algae were studied in the Arctic and

Antarctic. The assessment of photosynthetic parameters of

phytoplankton and sea ice algae from landfast sea ice of the

Chukchi Sea off Point Barrow, Alaska (spring 2005 -

spring 2006) showed that photosynthetic performance by

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ice algae was tightly linked to sea ice salinity, temperature,

and inorganic nutrient concentrations (mainly nitrogen)

(Manes and Gradinger, 2009). The capacity of Antarctic

bottom ice microalgae from the extremely low light habitat

of bottom ice to acclimate to different light conditions was

investigated experimentally (Mangoni et al., 2009).

Investigation of ice algae and phytoplankton food quality as

food source for two common Arctic macrobenthic species

showed that both consumer species had higher fatty acid

content and proportion of polyunsaturated components

when they were fed on ice algae compared to

phytoplankton, implying that ice algae has a higher food

quality (Sun et al., 2009). This was supported by a study

from Lake Baikal that showed that monoenoic fatty acids

have a much higher concentration in Ulothrix zonata

growing in the ice and at low temperature than in U. zonata

growing on the stony bottom (Osipova et al., 2009).

Trophic Interactions. Grazer periphtyon

interactions were investigated in freshwater and marine

habitats. A meta-analyses on grazer control of periphyton

biomass was conducted (Hillebrand, 2009). Gastropod

grazers were found to affected periphyton nutrient

stoichiometry in laboratory aquaria by changing benthic

algal taxonomy and through differential nutrient uptake

(Liess and Kahlert, 2009). Gastropod grazing has also been

shown to interact with light and nutrients in determining

benthic diatom species richness. These effects were mainly

mediated through changes in benthic algal productivity, but

periphtyon nutrient content and grazer activity also played

important roles (Liess et al., 2009a). Direct and indirect

effects of a potential aquatic contaminant, an ionic liquid,

on grazer-algae interactions indicated that sublethal

contaminant levels can negatively impact communities and

ecosystem processes (Evans-White and Lamberti, 2009).

Benthic consumer diversity indirectly changed periphtyon

nutrient content in marine rock pools, however diversity

effects were mainly due to the presence or absence of one

gastropod species, Littorina littorea (Hillebrand et al.,

2009). Experimental microcosms with artificially

constructed periphyton communities revealed the

importance of the benthic microbial food-web structure for

both top-down and bottom-up propagating effects of

consumers and resources, respectively (Fitter and

Hillebrand, 2009). No effect of predator richness on any

aspect of prey (benthic macro-and microalgae) structure

was found in a diverse marine food web (O'Connor and

Bruno, 2009). Experimental tests of the effects of grass

shrimp and nutrient addition on epiphytic algae in the

Grand Bay National Estuarine Research Reserve, revealed

that grass shrimp, more so than nutrient addition, altered

the community composition of epiphytic algae by

selectively grazing red algal epiphytes (McCall et al.,

2009). Lastly, it was found that natural densities of marine

mesograzers failed to limit growth of macroalgae or their

epiphytes in a temperate algal bed (Poore et al., 2009).

Disturbance and Stressors. Benthic algal

communities can also be affected by abiotic disturbances

and stressor, such as wave action, sediment and nutrients.

Artificial sheltering of exposed coast had a strong effect on

the structure and functioning of adjacent systems,

promoting a shift from consumer- to producer-dominated

communities. The effects included the replacement of

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barnacles, limpets and frondose algae by an increasing

cover of ephemeral algae (Martins et al., 2009). Removal

of algae on an intertidal mudflat reduced number of

animals and affected sediment properties (Murphy and

Tolhurst, 2009). Effects of inorganic sediment dose and

exposure time on stream macroinvertebrates and benthic

algae showed that relatively minor disturbances decreased

the organic proportion of epilithon significantly after the

first 24 h of exposure; however, algal biomass was reduced

significantly only after seven days (Molinos and Donohue,

2009). An investigation of repeated stressor episodes

(augmented nutrient inputs and increased sediments) on

algal communities in pasture streams found that algal

communities reacted more strongly to multiple

nutrient/sediment addition episodes than to rare or singular

episodes. This indicates a cumulative impact of

anthropogenic stressors on stream periphtyon (Riddle et al.,

2009).

Nutrient and Light Limitation. Both nitrogen

(N) and phosphorus (P), as well as light, carbon dioxide

(CO2) and silica (Si) can limit benthic algal growth alone or

in combination. It was found that atmospheric N

deposition may intensify P limitation of shallow epilithic

periphyton in unproductive lakes (Liess et al., 2009b) and

that P was most frequently the limiting nutrient in New

Zealand streams (McDowell et al., 2009). Both N and P

typically limit primary producers in oligotrophic streams

and rivers in the Pacific Northwest of the US, as suggested

by experiments on nutrient diffusion substrate (Sanderson

et al., 2009). Similar experiments with nutrient diffusing

substrata indicated also that periphyton metabolism was

related to both N and P availability, but that biomass

accumulation might have been limited primarily by N

(Scott et al., 2009). Field experiments in Florida Bay,

investigating the response of seagrass epiphyte

communities to N and P addition, found that P addition

resulted in significant changes in epiphyte community

structure, but community structure differed even more

between sites and times than between nutrient treatments

(Frankovich et al., 2009). A quantification of P and light

effects on stream algae found that P enrichment in streams

is likely to have its largest effect at concentrations < 25 µg

L-1 soluble reactive P, but only when streambed irradiances

were higher than 2 mol photons m-2 d-1 (Hill et al., 2009).

Marine experiments revealed a negative effect of giant kelp

on both light availability and understory algal abundance

(Arkema et al., 2009). A coupled hydrodynamic ecological

numerical model indicated that Artemia sp. grazing

phytoplankton was responsible for an increase in

photosynthetic available radiation reaching the pond floor

and the consequent increase in benthic algal biomass

(Bruce and Imberger, 2009). It was shown that elevated

levels of CO2 increased stream autotroph primary

productivity (Hargrave et al., 2009). Dissolved Si

depletion in the Garonne River in France was found to be

more severe where concentrations of dissolved nutrients

and chlorophyll a were high, suggesting that eutrophication

led dissolved Si depletion (Muylaert et al., 2009).

Biomonitoring and Bioassessment. Benthic

algal biomass, species composition and color, and in

particular benthic diatoms species composition have

emerged as a powerful tool for monitoring and assessing

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water quality in lakes and streams. Freshwater diatom and

macroinvertebrate diversity and community composition of

coastal permanent ponds along a gradient of human impact

in a Mediterranean eco-region show that diatoms tended to

reflect water chemistry through changes in community

structure, whereas invertebrates responded to physical

habitat changes primarily through changes in taxonomic

richness (Della Bella and Mancini, 2009). Similarly,

diatoms proved to be more useful in assessing agricultural

and coal mining impacts on streams than

macroinvertebrates and fish. Two new indices were

developed, a species-level Bray-Curtis (BC) similarity to

reference index and a genus-level diatom model affinity

(DMA) index to quantify agricultural and acid mine

drainage impacts on streams (Smucker and Vis, 2009).

And when algal communities, mainly diatoms, at sites

affected by acid mine drainage and in naturally alkaline

waters were compared, large differences in algal

community composition were found (Urrea-Clos and

Sabater, 2009). Investigating the impact of pesticide inputs

on the structure of riverine benthic diatom communities

with the help of the phytopixal approach, a means to assess

the spatial contamination potential, was a successful means

of discriminating diatom assemblages and provided

valuable information about pesticide exposure (Morin et

al., 2009). Diatom assemblages were also found useful in

distinguishing between particular land-use and water

quality types. Sites where high-intensity agriculture took

place were dominated by motile species of the genus

Nitzschia, and low-intensity agriculture was indicated by

motile species of the genus Navicula, whereas urban sites

contained a combination of species that were tolerant of

spikes in water quality (Walsh and Wepener, 2009). In

addition to diatom assemblages, other benthic algal types

can be important for biomonitoring. Benthic algal

cyanobacterial community and ecological and physical

characteristics were used to determine hikers’ impact on the

north fork of the Virgin River in Zion National Park, Utah

(Smith, 2009). Ecological responses to dam construction

by downstream benthic algal communities were examined

in a tributary of the Xiangxi River, China. The impacts of

dam construction on benthic algal communities took 2 to 3

y to emerge (Wu et al., 2009c). In a nitrogen-limited river

subject to Mediterranean summer drought hydrology, the

color of macroalgal proliferations changed with

successional and seasonal changes in epiphyte assemblages

(Power et al., 2009). Thus photogrammetric detection of

color changes in algal proliferations may help track reach

or basin-scale change in ecological functions.

The feasibility of using herbarium specimens to

validate reference conditions in the UK by comparing

diatom community composition of river sites with both

recent and historic diatom samples, was assessed (Yallop et

al., 2009). An integrated assessment of river health based

on water quality, aquatic life (attached algae and benthic

invertebrates) and physical habitat was devised (Meng et

al., 2009). A new index based on non-diatomaceous

benthic algae (acidification index periphyton, AIP) can be

used to describe the mean annual acidity of Norwegian

rivers. The AIP is most sensitive between mean annual pH

values of approximately 5.5 and 7.0 and can be especially

useful in detecting the first signs of an acidification trend or

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the last steps of a recovery process (Schneider and

Lindstrom, 2009). The results of an intercalibration among

European Union member states to compare national

approaches for setting ecological status boundaries in

phytobenthos assessment for the European Water

Framework Directive were described (Kelly et al., 2009a).

Based on a benthic diatom survey it was found that in order

to quantify the scale of temporal uncertainty associated

with benthic diatoms, the ecological status of a site should

be determined from a number of samples collected from

this site over a period of time (Kelly et al., 2009b). The use

of the ecosystem model AQUATOX to investigate

impairment thresholds keyed to biological indexes that can

be simulated, such as benthic chlorophyll a, was analyzed.

This kind of analysis was suggested as a way to evaluate

multiple contrasting impacts of hypothetical nutrient and

sediment reductions and to define nutrient criteria or target

concentrations that balance multiple management

objectives concurrently (Carleton et al., 2009). The public

opinion of what constitutes undesirable levels of benthic

algae in streams was surveyed in Montana. Results support

earlier work in the literature suggesting that chlorophyll a

levels of 150 mg m-2 represent a benthic algae nuisance

threshold (Suplee et al., 2009).

Pollution, Bioremediation and Nuisance Algae.

Metals and toxic substances as well as invasive algal

species can have strong effects on benthic productivity and

community structure, which can take a long time to reverse.

Copper and zinc addition in artificial stream channels

significantly reduced chlorophyll a concentrations, dry

mass and AFDM, and also changed benthic algal species

diversity and relative abundances of benthic algal species

(Atazadeh et al., 2009). Experiments investigated the

uptake properties of cadmium by Navicula pelliculosa mats

and found that diatom mats achieve concentrations that

could inhibit macroinvertebrate grazing (Irving et al.,

2009). The effects of sediment-associated toxins in the

River Elbe basin on benthic algae were analyzed.

Extraction with TENAX and subsequent effect-directed

analysis can help to prioritize contaminants and

contaminated sites with respect to the hazard of these

toxicants to green algae (Schwab et al., 2009). An

investigation into the toxicity of 1-alkyl-3-

methylimidazolium ionic liquids towards the benthic algal

species Bacillaria paxillifer and Geitlerinema amphibium,

found that short-chain compounds may pose a significant

risk to benthic ecosystems (Latala et al., 2009).

An evaluation of the spatial extent of the effects

of forest cover on stream ecosystems found that

maintenance or protection of reach and riparian buffers

alone will not sufficiently protect stream function and

structure from catchment-wide impacts (Stephenson and

Morin, 2009). After a decade of recovery form

acidification, several community attributes recovered fully,

but recovery of many aggregate functional and taxonomic

properties lagged behind. Potential causes of incomplete

algal recovery include incomplete chemical recovery and

the persistent absence of functionally important biota

(Turner et al., 2009). To reduce periphyton standing crops

in the Jackson River, pulsed flows can be used, but the

discharge required would probably need to produce

velocities of >100 cm s-1 (Flinders and Hart, 2009).

1913

The benthic diatom Didymosphenia geminata is

now considered a nuisance, bloom-forming and invasive

species in New Zealand. Experiments to investigate

invasion success of D. geminata found that it to be a mid to

late successional species that needs some pre-existing algal

growth to anchor to, whereas late successional stages of the

native periphyton community displayed partial resistance to

D. geminata invasion (Flöder and Kilroy, 2009). D.

geminata was also shown to alter benthic communities in

New Zealand rivers, since its presence was associated with

greatly increased periphyton biomass and, in most cases,

increased invertebrate densities and changes in invertebrate

community composition (Kilroy et al., 2009).

Algal Toxins and Algal Physiology. Benthic

algae can produce toxins that may pose a health threat to

humans, livestock and ecosystems in general. However

benthic algae may also produce defensive compounds that

are non-toxic. Effects and occurrences of algal toxins were

investigated and it was found that algal toxins of

Microcystis aeruginosa, and the dinoflagellate Akashiwo

sanguinea could slow down development or increase

mortality of mosquito larvae (Rey et al., 2009).

Microcystins from a Nostoc muscorum bloom occurring in

Ouka Meden River, Morocco, and their toxic effects were

identified and quantified. Their existence under these

particular environmental conditions was identified as a

potential human health hazard (Oudra et al., 2009).

Another toxic alga, the benthic diatom Cocconeis

scutellum, is producing one or more compounds

responsible for the early programmed cell death of the male

gonad and the androgenic gland of the shrimp Hippolyte

inermis. The metabolite composition of the compounds

was identified as trimethylsilyl (TMSi) derivatives!(Nappo

et al., 2009). The investigation of allelopathic interactions

in benthic biofilms found that the magnitude of the

response to allelochemicals depended on the target species

and the donor species as well as the abiotic conditions

under which they were growing (Leflaive and Ten-Hage,

2009).

Structural characteristics of the extracellular

matrix in the benthic green alga, Cosmarium reniforme

were found to be critical for survival in a biofilm

(Domozych et al., 2009). And last, phototrophic biofilm

samples from an Italian wastewater treatment plant were

studied in microcosm experiments under varying

irradiances, temperatures and flow regimes to assess the

effects of environmental variables on capsular

exopolysaccharides (Di Pippo et al., 2009).

Bacterial Ecology

Spatial and Temporal Patterns. Ammonia-

oxidizing archaea were more abundant than ammonia-

oxidizing bacteria in the sediments of a Chinese lake. The

sediment ammonia-oxidizing archaea community differed

from that in the water, but the ammonia-oxidizing bacteria

community was similar in both water and sediments (Jiang

et al., 2009a). Sediment ammonia-oxidizing bacterial

abundance and diversity was greater in the more eutrophic

basin of a Chinese lake (Chen et al., 2009d). Abundances

of different groups of sediment bacteria and activities of

alkaline phosphatase differed spatially in Chinese lakes

(Deng et al., 2009; Zeng et al., 2009). Fibrobacteres were

1914

found in relatively high abundance in lake sediments,

suggesting that these organisms may be important in

natural cellulose decomposition in lakes (McDonald et al.,

2009). Bacterial and viral densities were positively

correlated in Swedish lakes; sediments could be serving as

a viral reservoir (Sawstrom et al., 2009).

Spatial patterns in nutrient and organic matter

inputs appeared to drive riverine epilithic bacterial

composition (Kobayashi et al., 2009). Biofilm bacterial

community structure differed between urban and rural

streams (Lear and Lewis, 2009a). Sediment denitrification,

dissimilatory nitrate reduction, and anaerobic ammonia

oxidation rates varied spatially within an estuary; process

rates were correlated with functional gene abundances

(Dong et al., 2009). Lotic biofilm bacterial community

structure in two Japanese rivers were similar at all

freshwater sites, but differed between freshwater and

estuarine portions of the rivers (Honma et al., 2009).

Bacterial abundance in glacial meltwater stream sediments

increased with distance from the glacier. Isolated strains

varied with respect to optimal temperature, ionic strength

and pH, and produced different enzymes (Reddy et al.,

2009).

Bacterial community composition in the

sediments of Venice lagoon appears to be driven by urban

pollution and the presence of aquatic plants (Borin et al.,

2009). Bacterial community structure in mangrove swamp

sediments varied spatially and temporally; much variation

was correlated to sediment organic matter content (Zhang

et al., 2009b). Pigment-based analysis of marine wetlands

indicated that prokaryotic primary producers were co-

located with abundant sediment organic matter and/or

hypoxia (Janousek, 2009). The diversity of Bacteroidetes

differed among Chilean saline evaporitic basins (Dorador et

al., 2009).

An annual survey of microbial biomass (bacteria,

fungi, algae) and extracellular enzyme activity among

different benthic substrata (leaves, coarse and fine

substrata) in a Mediterranean stream revealed that bacterial

and fungal biomass were generally higher than algal

biomass, and that heterotrophic microbial activity peaked in

autumn (Artigas, et al. 2009). Wetland heterotrophic

(bacterial and fungal) microbial community composition

differed greatly among water, sediment, plant litter, and

epiphytic habitats. Seasonal changes were relatively small

(Buessing et al., 2009). Bacteria in the surface sediments

of a wetland were best able to use plant litter decay

products; bacteria from deeper within the sediments could

use less labile carbon sources (Salomo et al., 2009).

Prokaryotic community structure varied with sediment

depth; Archaea were only present at deeper areas.

Extracellular enzyme activity also generally declined with

depth (Jackson and Vallaire, 2009). Depth profiles of

methanotroph abundance and methane oxidation activity

differed between the littoral and profundal sediments of

Lake Constance (Rahalkar et al., 2009). Bacteria (and

fungi) were much more abundant in surface sediments

versus subsurface layers in a constructed vertical flow

wetland (Zhou et al., 2009b). Bacterial community

composition in Lake Taihu sediments did not vary strongly

with sediment depth, but Archaeal community composition

did vary (Ye et al., 2009). Sulfate-oxidizing bacteria were

1915

most abundant in the surficial sediments of the Pearl River

estuary; in contrast, numerous novel sulfate-reducing

prokaryotes were distributed throughout the sediments

(Jiang et al., 2009b). Sediment bacterial communities in

the Changjing estuary and Coastal East China Sea had

greater diversity than bacterioplankton. Sediment bacterial

communities did not differ spatially, but did exhibit

seasonal patterns (Feng et al., 2009). Sediment bacterial

communities in the saline Salton Sea were similar to typical

marine sediment communities, and differed from local

bacterioplankton communities (Dillon et al., 2009). Active

communities of abundant methanotrophs were found in

Lake Baikal thermal springs (Zelenkina et al., 2009).

Numerous bacterial strains have been recovered from Lake

Baikal oil seepage zones (Lomakina et al., 2009). Lanoil et

al. (2009) reported the first direct evidence for microbes

from beneath the Antarctic ice sheet.

Lake sediment extracellular enzyme activities

were generally elevated in macrophyte-dominated areas.

Aerobic bacteria dominated surficial sediments (Zhou et

al., 2009a). Macrophyte presence and senescence

stimulated the abundance and activity of ammonifying

bacteria, ammonium-oxidizing microbes, and nitrate-

oxidizing bacteria in an Egyptian lagoon (Dewedar et al.,

2009). Release of oxygen into sediments by macrophytes

may have caused a stimulation of ammonia-oxidizing

Archaeal densities (Herrmann et al., 2009). Nitrifying

activity on macrophyte shoots was greatest on mature

shoots, possibly because of well-developed epiphyte

communities (Palijan et al., 2009). Nitrate reduction and

nitrification activities were greater in the rhizosphere than

in unvegetated sediments (Ruiz-Rueda et al., 2009).

Denitrifying bacteria community structure also differed

between these two habitats. Community structure of acid

mine drainage biofilms was related to functional gene

expression (Wilmes et al., 2009). Ammonia-oxidizing

bacteria were much more common and more active than

ammonia-oxidizing Archaea in a Danish estuary

(Magalhaes et al., 2009). Salmonella isolates in the North

American Great Lakes showed spatial and interannual

variation, and were often associated with the green alga

Cladophora (Byappanahalli et al., 2009).

Biofilm bacterial community composition

differed from bacterioplankton in Lake Biwa. Interstitial

biofilm water was much richer in nutrients and lower in

N:P ratio than lake water (Tsuchiya et al., 2009). Small-

scale hydrodynamics explained almost half of the variance

in stream bacterial community composition (Besemer et al.,

2009a). Microscale differences in stream bacterial biofilm

architecture were related to micro-scale distribution of

individual bacterial taxa (Besemer et al., 2009b). Rehmann

and Soupir (2009) produced a model of how sediment

bacterial communities affect suspended microbes in

streams.

Biotic Interactions. Nutrient availability

affected the coupling of surface-associated algae and

bacteria. In two separate studies (Ziegler et al., 2009; Lyon

and Ziegler, 2009), bacteria in low-nutrient systems

retained a greater proportion of algal production. Biofilm

bacterial and algal production were tightly correlated, but

this relationship could be weakened by provision of excess

labile carbon (Ylla et al., 2009). Strong relationships

1916

existed between algal biomass and bacterial abundance and

production in illuminated periphyton, but were very weak

in shaded periphyton. Greater availability of external

organic carbon in shaded periphyton most likely caused the

weak algal-bacterial coupling under low light (Rusanov et

al., 2009).

A gastropod grazer consistently increased

sediment bacterial densities, probably through some

combination of fertilization, bioturbation and food web

alteration (Pillay et. al., 2009). Trophic transfer of

pathogenic bacteria from aquatic biofilms through grazing

stoneflies to trout was shown to be a possible infection

route for furunculosis (Adams et al., 2009). The role of

aquatic biofilms in Legionella outbreaks was reviewed

(Lau and Ashbolt, 2009). Bacteriovorax survival in the

face of salinity and temperature extremes was greatly

enhanced by association with biofilms (Williams et al.,

2009). Berdjeb et al. (2009) reviewed the effects of viruses

on aquatic ecosystems. Exposure to single-species versus

mixed-species leaf leachate generally had little effect on

aquatic bacterial community composition, but certain plant

taxa did appear to produce compounds that could strongly

alter bacteria communities (Wu et al., 2009a). Invasion by

Spartina alterniflora generally reduced the diversity of

sulfate-reducing bacteria in a Chinese wetland; however

some increases in sulfate-reducing bacterial diversity were

observed when S. alterniflora became senescent (Nie et al.,

2009).

Biogeochemistry. Both arsenic-reducing and

arsenic-oxidizing bacteria were isolated from arsenic-

contaminated river sediments; the activity of these bacteria

should influence arsenic biogeochemistry (Escalante et al.,

2009). A marine bacterium capable of both arsenate

reduction and arsenite oxidation was isolated from

hydrothermal sediments (Handley et al., 2009).

Bacterially-mediated mercury methylation was stimulated

by cysteine addition (Schaefer and Morel, 2009). Iron held

in the mineral vivianite could be oxidized by anaerobic

nitrate-reducing bacteria (Miot et al., 2009). Nitrate-

dependent iron oxidation can supplement the energy

metabolism of nitrate-reducing bacteria, and contributes to

iron cycling in anaerobic lake sediments (Muehe et al.,

2009). Manganese and iron, in addition to sulfate, can

serve as terminal electron acceptors for anaerobic

methanotrophs (Beal et al., 2009). Microbial activity is

unlikely to fix rhenium in aquatic sediments (Dolor et al.,

2009). Models incorporating microbial cellular energy

conservation accurately predict sulfate chemistry in lake

sediment pore water, whereas common thermodynamic

models do not (Jin and Bethke, 2009). Microbial activity

altered the N content of detrital material in the Amazon

River (Tremblay and Benner, 2009). Nitrate removal from

the hyporheic zone of an Alaskan river was dominated by

plant and microbial uptake; losses to denitrification were

minor (Pinay et al., 2009)

Nutrient Removal. Density of ammonia-

oxidizing bacteria predated denitrification potential in the

sediments of a hydroponic biofilter (Li et al., 2009a). In a

polluted urban stream, nitrification occurred mainly in

sediments, and was constrained by the abundance of

nitrifying bacteria (Jiao et al., 2009). Planted wastewater

treatment wetlands had significantly higher nutrient

1917

removal rates due to much greater abundance of sediment

bacteria (Kantawanichkul et al., 2009). The abundance of

sediment nitrifying bacteria was highly correlated to

ammonia removal rates in a constructed wetland (Xie et al.,

2009). Sediment bacterial communities contained slower-

growing taxa than water column communities, but were

key regulators of nutrient transformation (Schneider and

Topalova, 2009).

Pollution and Bioremediation.

Gammaproteobacteria from Great Salt Lake sediments

were effective degraders of hydrocarbons over a wide

salinity range (Sei and Fathepure, 2009). The herbicide

diuron rapidly reduced algal photosynthetic activity, and

also negatively affected bacteria in lotic biofilms (Ricart et

al., 2009). Mixed substrates and co-cultures of bacterial

strains greatly altered degradation of organic contaminants

(Horng et al., 2009). A substrate-addition respiration

change assay was able to measure potential polycyclic

aromatic hydrocarbon degradative ability of natural

sediment microbial communities (Gu et al., 2009). River

sediments were hot spots for microbial degradation

potential for chlorinated aliphatic hydrocarbons (van der

Zaan et al., 2009). Abundance of hexachlorobenzene-

degrading bacteria in river sediments was affected by

several environmental variables, including

hexachlorobenzene contamination (Tas et al., 2009). Most

prokaryotic phylotypes recovered from metal-contaminated

river sediments in Idaho showed great similarity to know

cultivable lineages from other contaminated environment;

however, one Euryarchaeotan phylotype showed no close

similarity to any known taxon (Rastogi et al., 2009).

Biodegradation of PCB in sediments was enhanced by

bioaugmentation with the bacterial strain Pseudomonas

stutzeri (Dercova et al., 2009). Epilithic biofilms and

sediments downstream of diuron runoff from vineyard

showed some adaptation to diuron exposure (Pesce et al.,

2009b). Many bacteria contributed to nonylphenol

degredation in mangrove sediments; addition of a variety of

substances stimulated or inhibited degradation rates (Chang

et al., 2009). Addition of slowly degrading polybrominated

hydrocarbons to river sediments greatly altered bacterial

communities. In contrast, addition of a degradable

polybrominated hydrocarbon did not alter bacterial

community structure (Yen et al., 2009). Polycyclic

aromatic hydrocarbon-degrading genes were most common

in Lake Erie sediments with a history of hydrocarbon

contamination, however, some degradative genes were

ubiquitously distributed (DeBruyn et al., 2009). Exposure

to triclosan and triclocarban altered algal, bacterial,

polysaccharide, and micrometazoan components of aquatic

biofilms (Lawrence et al., 2009). Increased nutrient levels

in sediments changed the toxic effects of pyrene from

alteration of community structure to alteration of

community function (Petersen, et al. 2009). Realistic levels

of titanium oxide nanoparticles compromised microbial cell

membranes in aquatic systems (Battin et al., 2009). Fish

farm pollution altered sediment bacterial community

structure, but did not extirpate beta-ammonia oxidizing

bacteria (Bissett et al., 2009).

Metals/Toxins. Neutrophilic heterotrophs were

important iron reducers in a German lake (Porsch et al.,

2009). Arsenite-oxidizing genes and activity were

1918

observed in Chilean stream sediments (Valenzuela et al.,

2009). Interactions of Phragmites and its rhizosphere

bacteria sped the removal of bisphenols from sediments

(Toyama et al., 2009). Sulfate and metals from acid mine

drainage reduced bacterial physiological activity (Kim et

al., 2009). Glyphosate exposure had limited and

seasonally-dependent effects on lotic microbial

communities (Pesce et al., 2009a). A strain of acid-tolerant

sulfate-reducing bacteria may prove useful in remediating

heavy metals from acid mine drainage (Senko et al., 2009).

Microcystin-degrading bacteria were observed in a Chinese

lake (Song et al., 2009).

Fecal Bacteria. Sediments in Lake Geneva can

serve as a permanent reservoir of fecal bacteria (Pote et al.,

2009; Haller et al., 2009b). Fecal bacteria survived for

long periods of time (>50 days) in freshwater sediments,

and grew best in silty environments (Haller et al., 2009a).

Sediment-associated fecal bacterial growth may be limited

by carbohydrate (Toothman, et al., 2009). Resuspension of

stream sediments by wading greatly increased water

column fecal bacterial concentrations (Phillip et al., 2009).

Dessication and temperature were important for

deactivation of fecal bacteria in beach sands. Mechanical

grooming had no effect (Mika et al., 2009).

Antibiotics and Antibiotic Resistance.

Antibiotics introduced to aquatic systems as animal feed

resulted in more bacterial resistance than antibiotics

administered directly to feces (Yu et al., 2009). The

tetracycline resistance gene tet39 can be found in a much

wider range of environmental bacteria than previously

thought (Adelowo and Fagade, 2009). Biofilms were very

important reservoirs of antibiotic resistance genes (Zhang

et al., 2009c).

Biomonitoring. The sulfur bacterium

Chromatium showed potential as a bioindicator of crude oil

pollution in sediments (Essien and Antai, 2009). Stream

epilithic bacterial community composition was not as

sensitive a bioindicator as microinvertebrate communities

(Lear et al., 2009a). In contrast, epilithic bacterial

community structure could serve as a bioindicator for

pollution by acid mine drainage (Lear et al., 2009b).

General. Bert et al. (2009) reviewed microbial

processes involved in phytoremediation. The capping

material used to cover sediments had an influence on

microbial activity in sediments (Wang et al., 2009b).

Saltwater intrusion into freshwater sediments altered

metabolic activity. On a timescale of weeks, such changes

resulted from altered gene expression, not shifts in

community structure (Edmonds et al., 2009). Freshwater

sediments accumulate and served as a reservoir for

bacteriophages (Skraber et al., 2009).

Biofilm bacteria, via production of extracellular

polymers, stabilize aquatic sediments, and thus should be

considered “ecosystem engineers”. Algal-bacterial

interactions could be important to such sediment

stabilization (Gerbersdorf et al., 2009). Biofilm

development was the primary stabilizing factor for fine

sediment types; biofilm structure and extracellular

polymers appeared to be stabilizing mechanisms (Droppo,

2009). Production of extracellular polymers was the most

important factor for promoting bacterial biofilm formation

(Li et al., 2009b). Overexpression of the galE gene

1919

promoted production of extracellular polymers and biofilm

formation (Niou et al., 2009). Similarly, overexpression of

the VpsS gene promoted biofilm formation in Vibrio

cholerae by activating components of the quorum-sensing

pathway and production of extracellular polymers

(Shikuma et al., 2009). Exposure to calcium reduced the

expression of genes for extracellular polymer production by

Vibrio cholerae and led to biofilm dissolution (Bilecen and

Yildiz, 2009).

Microbial iron reduction led to redox-mediated

precipitation of dissolve copper and subsequent galvanic

corrosion of steel pilings in Lake Superior (Ray et al.,

2009). A sulfur bacterium closely related to Thioploca

ingrica was isolated from Lake Baikal sediments

(Zemskaya et al., 2009). Exposure to UV radiation reduced

the proportion of viable bacteria in wetland biofilms

(Thomas et al., 2009). Exposure to light eliminated

chlorophyll-containing prokaryotes from laboratory

biofilms (Lear et al., 2009c). Community structure of river

biofilms appeared to be more sensitive to abiotic than biotic

factors (Paule et al., 2009).

Fungal Ecology

Spatial and Temporal Patterns. A survey of

brackish Egyptian lakes found fungal diversity to decrease

with increasing salinity (El-Sharouny et al., 2009). Organic

matter was correlated to fungal diversity in four Polish

ponds (Godlewska et al., 2009). Plant seeds were good

habitat for nearly 100 species of fungi (Czeczuga et al.,

2009b). Fungal communities on leaf litter differed strongly

between riffle and pool habitats in a tropical stream

(Rincon and Santelloco, 2009). Spatial and temporal

variation in fungal colonization suggested that benthic

algae exude substances that can stimulate or inhibit fungi

Czeczuga et al. (2009a). Aquatic fungal community

composition differed over both a temperate-subtropical

gradient, and between woody and herbaceous substrata

(Raja et al., 2009a). A survey of aquatic fungi in three

Venezuelan rivers found that fungal floras differed between

rivers and through time, but did not observe seasonal

changes (Da Silva and Briedis, 2009). Barlocher (2009)

considered competing hypotheses for aquatic fungal

dispersal, and argued for the use of molecular techniques to

test these hypotheses.

Biotic interactions and decomposition.

Conditioning of leaf litter by fungi increased its palatability

for the mysid Limnomysis benedeni (Assmann et al., 2009).

Gammarus fossarum preferred eating leaf discs exposed to

antibiotics, possibly as a result of the greater fungal

biomass on these leaves (Bundschuh et al., 2009). In

contrast, fungal extracts inhibited leaf consumption by

Gammarus roeselli (Assmann and von Elert, 2009). Fungal

abundance on leaves did not affect the preference of the

Trichopteran shredder Pycnopsyche, but did increase its

growth (Chung and Suberkropp, 2009a); fungal C

accounted for 50-100% of insect growth (Chung and

Suberkropp, 2009b).

Fungal and bacterial community composition of

submerged leaf litter appeared to be regulated by different

factors (Harrop et al., 2009). Bacteria and fungi on leaf

litter engaged in agonistic interactions, reduced growth and

enzyme activity (Baschien et al., 2009). Mixing of leaf

1920

litter species can affect fungal diversity on submerged litter

(Kominoski, 2009). Fungal biomass and leaf

decomposition was measured in an Oman stream. Despite

an impoverished fungal flora (14 species), decomposition

rates were similar to those observed in temperate and

tropical streams (Al-Riyami et al., 2009). Along with litter

quality, fungal biomass was an important predictor of litter

breakdown rates (Hladyz et al., 2009).

Abiotic influences. Freeze-thaw treatment

reduced fungal diversity and litter decay, whereas a 7°C

elevation in temperature increased decay rates (Fernandes

et al., 2009b). A 5°C temperature increase, coupled with

increased diel temperature fluctuations, accelerated litter

decomposition, apparently by increasing fungal growth

(Dang et al., 2009). Temperature and osmotic potential

interactively controlled fungal growth (Palmero et al.,

2009). Dam decommissioning in Fossil Creek, Arizona

restored natural flow regimes. Fungal communities quickly

responded to the restored flow, but litter decomposition did

not (Muehlbauer et al., 2009). Sudden flow reductions

reduced fungal biomass and sporulation, but these effects

were conditioned on the presence of invertebrate shredders

(Schlief and Mutz, 2009). Comparison of leaf litter from a

high- and a low-nutrient stream revealed lower fungal

diversity in the high-nutrient stream. Fungal communities

in a reciprocal transplant experiment remained similar to

those of the original stream (Sridhar et al., 2009). Fungal

biomass and reproduction were affected by stream trophic

state; in hypertrophic streams, fungal biomass and

reproduction were reduced (Duarte et al., 2009b).

Exposure to zinc and/or copper reduced fungal diversity

and litter decomposition, but not fungal biomass

(Fernandes et al., 2009a; Duarte et al., 2009a), and can

cause programmed cell death in fungi (Azevedo et al.,

2009). Acid mine drainage reduced litter breakdown and

altered fungal community composition (Niyogi et al.,

2009). Reduced pH slowed litter decomposition but did not

affect fungal diversity (Simon et al., 2009).

Bioremediation. Haritash and Kaushik (2009)

reviewed the importance of microbes, including aquatic

bacteria and fungi, for biodegradation of polycyclic

aromatic hydrocarbons. Extracellular laccase activity and

intracellular reactions were of equal importance for aquatic

fungal biodegradation of an environmental estrogen

(Martin et al., 2009).

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 Water Environment Research, Volume 82, Number 10—Copyright © 2010 Water Environment Federation 
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Li, M. Y.; Zhang, J.; Lu, P.; Xu, J. L.; Li, S. P. (2009b) 
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Malkin, S. Y.; Sorichetti, R. J.; Wiklund, J. A.; Hecky, R. 
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 Water Environment Research, Volume 82, Number 10—Copyright © 2010 Water Environment Federation 
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Manes, S. S.; Gradinger, R. (2009) Small Scale Vertical 
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the Influence of Extracellular Laccase and 
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McDowell, R. W.; Larned, S. T.; Houlbrooke, D. J. (2009) 
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Miot, J.; Benzerara, K.; Morin, G.; Bernard, S.; Beyssac, 
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1934

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Phycologia, 48 (2), 130–135.

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Pasternak, A.; Hillebrand, H.; Floder, S. (2009)

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 Water Environment Research, Volume 82, Number 10—Copyright © 2010 Water Environment Federation 
1936 
Benthic Community Structure in a Marine-
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Porsch, K.; Meier, J.; Kleinsteuber, S.; Wendt-Potthoff, K. 
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Ramamoorthy, S.; Piotrowski, J. S.; Langner, H. W.; 
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 Water Environment Research, Volume 82, Number 10—Copyright © 2010 Water Environment Federation 
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(2009) Ecology of Sulfate-Reducing Bacteria in an 
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Mastogloia Smithii Var. Lacustris Grun.: A Structural Engineer of Calcareous Mats in Karstic Subtropical Wetlands.

Article

Nov 2010

.-Mastogloia smithii var. lacustris Grun. is the dominant diatom in periphyton mats of the calcareous, freshwater to brackish wetlands of Caribbean coasts. Despite oligotrophy, frequent desiccation, high irradiance and temperatures, and occasional fire, periphyton communities in these wetlands can produce over 2000 g m 2 of organic biomass, prompting studies that examine stress resistance and maintenance of algal mats under extreme conditions. The diatom flora inhabiting periphyton mats from over 500 sites in the Florida Everglades and similar wetlands in Belize, Jamaica and Mexico was examined, and M. smithii var. lacustris was a persistent component, present in 97% of samples and comprising up to 80% of a diverse diatom assemblage. Valves at various stages of division were observed encased in extracellular polysaccharide that exceeded the cell volume; SEM observations confirm issuance from mantle pores resulting in suspension of the cell in a matrix dominated by cyanobacterial filaments. Using corresponding biophysical data from the collection sites, we define the optima for M. smithii var. lacustris along salinity, pH, phosphorus, and water depth gradients. Experiments revealed a collapse of M. smithii var. lacustris populations in the presence of above-ambient phosphorus concentrations and a rapid resurgence upon reflooding of desiccated mats. This widespread diatom taxon appears to play a critical role similar to that of cyanobacteria in microbial mats, and its disappearance in the presence of enrichment threatens biodiversity and the natural function in these systems that are increasingly influenced by urbanizat

Color quantification in the study of biofilm formation on granite stone in historical and artistic heritage

Thesis

Full-text available

Jul 2012

Patricia Sanmartín

The Fungal Community of Lake Sjenica, Serbia Branislav Ranković Journal of Freshwater Ecology - J FRESHWATER ECOL. 01/2004; 19(2):325-332.

Article

Jan 2004

Branislav R Ranković

ABSTRACT From water samples collected throughout the year from Lake Sjenica, four hundred and eighty cultures of filamentous fungi (Zygomycotina, Ascomycotina, and Deuteromycotina) were isolated. These comprised 44 species from 16 genera, the dominant of which were Penicillium and Aspergillus. The average number of spores per liter of water was relatively high, with maximum of 7,050 in March and a minimum of 451 in July. The number of spores and the number of isolates were both greatest in samples taken in March and September. Some differences in vertical distribution were present. The community of autochthonous aquatic fungi was made up of the species Achlya americana, A. racemosa, Dictyuchus sterile, Leptomitus lacteus, Pythium ultimum, Saprolegnia ferax, S. hypogyna, and S. monica. No regularity was discernible in the distribution of these fungi.

Biological Criteria for Inland Freshwater Wetlands in Florida: A Review of Technical & Scientific Literature (1990-1999)

Article

Spectrophotometric color measurement for early detection and monitoring of greening on granite buildings

Article

Full-text available

Mar 2012
BIOFOULING

This paper addresses the detection and monitoring of the development of epilithic phototrophic biofilms on the granite façade of an institutional building in Santiago de Compostela (NW Spain), and reports a case study of preventive conservation. The results provide a basis for establishing criteria for the early detection of phototrophic colonization (greening) and for monitoring its development on granite buildings by the use of color changes recorded with a portable spectrophotometer and represented in the CIELAB color space. The results show that parameter b* (associated with changes of yellowness-blueness) provides the earliest indication of colonization and varies most over time, so that it is most important in determining the total color change. The limit of perception of the greening on a granite surface was also established in a psycho-physical experiment, as Δb*: +0.59 CIELAB units that correspond, in the present study, to 6.3 μg of biomass dry weight cm(-2) and (8.43 ± 0.24) × 10(-3) μg of extracted chlorophyll a cm(-2).

Color measurements as a reliable method for estimating chlorophyll degradation to phaeopigments

Article

Full-text available

Jul 2011
BIODEGRADATION

The application of biocides is a traditional method of controlling biodecay of outdoor cultural heritage. Chlorophyll degradation to phaeopigments is used to test the biocidal efficacy of the antimicrobial agents. In the present study, the usefulness of color measurements in estimating chlorophyll degradation was investigated. An aeroterrestrial stone biofilm-forming cyanobacterium of the genus Nostoc was chosen as test organism, comparing its different behaviour in both planktonic and biofilm mode of growth against the isothiazoline biocide Biotin T®. Changes in A(435 nm)/A(415 nm) and A(665 nm)/A(665a nm) and in the chlorophyll a and adenosine triphosphate (ATP) cell content were compared with the variations in the CIELAB color parameters (L*, a*, b*, C*(ab) and h(ab)). Our findings showed that both the phaeophytination indexes are useful in describing degradation of chlorophyl a to phaeopigments. Moreover, the CIELAB color parameters represented an effective tool in describing chlorophyll degradation. L* CIELAB parameter appeared to be the most informative parameter in describing the biocidal activity of Biotin T® against Nostoc sp. in both planktonic and biofilm mode of growth.

Relationship between color and pigment production in two stone biofilm-forming cyanobacteria (Nostoc sp PCC 9104 and Nostoc sp PCC 9025)

Article

Full-text available

Jul 2010
BIOFOULING

Previous studies have provided evidence that color measurements enable on site quantification of superficial biofilms, thereby avoiding the need for sampling. In the present study, the efficiency of color measurements to evaluate to what extent pigment production is affected by environmental parameters such as light intensity, combined nitrogen and nutrient availability, was tested with two cyanobacteria, Nostoc sp. strains PCC 9104 and PCC 9025, which form biofilms on stone. Both strains were acclimated, in aerated batch cultures for 2 weeks, to three different culture media: BG-11, BG-11(0), and BG-11(0)/10 at either high or low light intensity. The content of chlorophyll a, carotenoids, and phycocyanins was measured throughout the experiment, together with variations in the color of the cyanobacteria, which were represented in the CIELAB color space. The results confirmed that the CIELAB color parameters are correlated with pigment content in such a way that variations in the latter are reflected as variations in color.

Characteristics and mechanisms of the hydroponic bio-filter method for purification of eutrophic surface water

Article

Full-text available

Nov 2009
ECOL ENG

The hydroponic bio-filter method (HBFM) was adopted to purify eutrophic surface water. The average removal efficiency of total nitrogen (TN) and total phosphorus (TP) was 16.8% and 30.8%, respectively, at the hydraulic loading rate (HLR) of 3.0 m3 (m2 d)−1. The mass removal rate of TN and TP accordingly reached 1.0 and 0.1 g (m2 d)−1 separately. The sedimentation of particulate nitrogen and phosphorus played a major role in removal of nitrogen and phosphorus, which contribute 62.2% and 75.9%, respectively. The optimal HLR of HBFM ranged from 3.0 to 4.0 m3 (m2 d)−1. The sediment in midstream reached a maximum nitrification potential of 4.76 × 10−6 g (g h)−1, while upstream it reached a maximum denitrification potential of 8.1 × 10−7 g (g h)−1. The distribution of nitrification potential corresponded to the ammonium-oxidizing bacteria density. The key for improving nitrogen removal efficacy of HBFM system consisted of changing the nitrification/denitrification region distribution and accordingly enhancing the denitrification process. The sum of dissolved nitrogen removed by denitrification and plant assimilation was nearly equal to the amount released by sediment. Secateur length of Nasturtium officinale had some effect on its uptake rate. The length of cut should be less than 10 cm at a time. The harvesting frequency of once a month for N. officinale had no influence on nitrogen and phosphorus removal.

Registry of aquatic hyphomycetes in mountain coast rivers, Venezuela

Article

Full-text available

Aug 2009
INTERCIENCIA

Aquatic hyphomycetes are microscopic imperfect fungi and are the principal decomposers of the submerged organic matter in rivers. Consequently, they are involved in the cycling of nutrients and energy provision at the first trophic level of the lotic system. Although this group of fungi have an ample geographic distribution, few studies have been performed in Venezuela. Therefore, a monthly registry of the hyphomycetes species in three rivers of the Mountain Coast (Cabriales River, Cúpira River and Quebrada Tócome) was carried out. The results indicate that the flora of aquatic hyphomycetes is varied in each river and the same fluctuated in number of species during the study, nevertheless, a seasonal tendency was not observed during the year.

Effects of agriculture on the abundance and community structure of epilithic algae in mountain streams of subtropical Taiwan

Article

Full-text available

Jan 2009
BOT STUD

This study aimed to characterize the abundance and community structure of epilithic algae and to examine the effects of intensive agriculture in mountain streams of the Wuling area. There were significant seasonal variations in epilithic algal biomass, with higher values in spring and winter and lower values in summer and fall. Effects of agriculture on the subtropical streams of the Wuling area were significant and varied with the extent of agriculture in the catchment. The biomass was significantly higher in Yousheng Stream with a larger area of agriculture than in other streams. Diatoms were the most abundant species, contributing over 85% to the total cell number. Most of these were pennatae diatoms, of which the genus Achnanthidium was the most abundant in the area. However, the communities showed clear seasonal and spatial changes. BIOENV analysis suggested that the combination of water temperature, conductivity, NO 2+NO 3 and SiO 2 concentrations and current velocity comprised the major factors explaining seasonal changes in the community, while the combination of NO 2+NO 3 and SiO 2 concentration and grazer density comprised the major factors affecting spatial changes. Changes in abundance and community structure of epilithic algae can be used to monitor the effects of agriculture in tropical/subtropical mountain streams.

Testing molecular tools for assessment of taxonomic composition of a benthic algal community

Article

Jan 2009
NOVA HEDWIGIA

Molecular assessments of algal biodiversity have the potential for more automated, complete and accurate characterization of taxa in natural communities than morphological assessments by microscopy. We used molecular tools to isolate, characterize, and taxonomically identify genetic sequences; and then we compared taxa identified molecularly to those identified microscopically with morphological characters. These analyses were conducted on a single benthic algal community from a stream. Both bacterial and eukaryotic sequences were targeted with domain-specific primers for 16S and 18S rRNA genes and 90 percent of the sequenced data was potentially identifiable. The 16S library revealed that 23 % of the prokaryotic isolates were photosynthetic (Cyanophyta). Two genera of cyanobacteria were observed microscopically in the sample, but they were rare. No cyanobacteria were reliably identified at the genus level using molecular techniques. For the eukaryotic community 13 % of the sequences corresponded with the phototrophic taxa using 18S sequences. All eukaryotic, phototrophic taxa were identified reliably, i.e. with greater than or equal to 98 % similarity with sequence data. Four of the five eukaryotic genera and three species were identified molecularly among the 53 species identified with morphological characteristics. While species level matching with the two techniques was not as high as expected, the data suggest that genus level identification might be attained with more comprehensive databases. Considerable work is required to document RNA sequences for more taxa and to evaluate variability in sequences within and among taxa to improve both molecular and morphological identification of algae.

Diversity of the genera of pennate diatoms in the Punjab

Article

Oct 2009

Twenty nine genera of algae belonging to 15 families of the phylum Bacillarophycota were collected during December 2003 and July 2006 from different freshwater habitats in various districts of the Punjab Province of Pakistan. Among them family Pinnularaceae with 19 species was most commonly found (25.33%), next to it were the families Cymbellaceae (13.33%), Naviculaceae (13.33%) and Nitzschaceae (12%) with 9 or 10 species each. The genera Cymbella with 10 species (13.33%), Nitzschia with 9 species (12%), Navicula and Pinnularia with 8 species each (10.66%) occurred most commonly. About 64% of diatoms were found as epiphytes, 22.66% as planktic and epiphytic both, and 13.33% as pure planktic individuals. Greatest proportion of collections (89.33%) were made from Lahore City and its neighbouring areas, which was followed by the districts of Gujranwala (24%) and Kasur (20%). Most of the diatoms were collected in winter (42.66%), smallest number of them were found in autumn (10.66%), while in rest of the two seasons they occurred in almost equal proportions (25.33 & 26.66%).

Benthic Algae (Except Bacillariophyta) and Their Seasonal Variations in Karagol Lake (Borcka, Artvin-Turkey)

Article

Jan 2009

Seasonal variation in the species composition of the benthic algae of Karagöl Lake was investigated from April to October in 2001 and 2002. The benthic algal flora consisted of 38 taxa belonging to the divisions Chlorophyta, Cyanophyta, Euglenophyta, and Chrysophyta. In general, Chlorophyta were dominant in terms of species number and abundance during the study period. The distribution range of the benthic algae composition and dominant species differed from each other at all stations. Benthic algal growth was mostly influenced by water temperature and light.

PAH-biodegradation potential of indigenous microorganisms: Evidence from the respiratory activity of surface sediments in the Quanzhou Bay in China

Article

Jan 2009

Seven stations were established in the Quanzhou Bay (24.73°-24. 96°N, 118.50°-118.70°E) in China on three cruises to determine the concentrations of polycyclic aromatic hydrocarbons (PAHs) and the numbers of PAH-degrading bacteria in surface sediments. Assessing the biodegradation potential of indigenous microorganisms by measuring the respiratory intensity with the addition of PAHs in sediment samples was also one of the aims of this study. The results show that the total PAH concentrations of the sediments were 99.23-345.53 ng/g dry weight (d.w.), and the PAHs composition pattern in the sediments was dominated by phenanthrene, fluoranthene and pyrene. The numbers of phenanthrene, fluoranthene and pyrene-degrading bacteria during three cruises were 1.42 × 10 3-8.93 × l0 4 CFU/g d.w., 8.29 × 10 3-9.43 × 10 4 CFU/g d.w. and 7.05 × l0 3-9.43 × 4 CFU/g d.w., respectively. The addition of three model PAH compounds (phenanthrene, fluoranthene and pyrene) showed a great influence on the increasing of the microbial activity in the sediments. And there was a significant correlation among the change of respiratory activity, PAH concentration and the number of PAH-degrading bacteria. The change in respiratory activity under PAHs selective pressure could, to a certain extent, indicate the potential degradative activity of the PAH-degrading microbial community.

Characteristics of fattyacid methyl esters (fames) and enzymatic activities in sediments of two eutrophic lakes

Article

Jan 2009

Enzymatic activities and fatty acid methyl esters (FAMEs) in the sediments of two eutrophic lakes in Wuhan city were investigated. The results showed phosphatase and dehydrogenase activities in the lotus zone and plant floating bed zone were significantly lower than those in other sites, and urease activity was the highest where microorganism agents were put in. Fatty acid group compositions indicated the predominance of aerobic bacteria in the surface sediments in shallow lakes. The ratios of FAMEs specific for bacteria and Gram-positive bacteria exibited significant differences between the two lakes. The results of trans to cis indicated that the microorganisms in Lake Yuehu could adapt themselves to environmental stress better. The enzymatic activities and FAMEs showed differences in different sites, indicating that ecological restoration measures and environmental conditions could affect lake sediment to some extent. But the monitoring work would be done in series to exactly evaluate the effect of the remediation measures.

Fungi and straminipilous organisms found in ponds in Białystok

Article

Jan 2009
POL J ENVIRON STUD

Our study involved the quantitative analysis of species composition of fungi and straminipilous organisms in four ponds situated in Biatystok, Poland. The observations performed in April and November 2006 with respect to hydrochemical conditions revealed the occurrence of 48 species, including 9 fungi and 39 straminipilous organisms. Among species of fungi and straminipilous organisms, we found such pathogens of crustaceans and fish as Achlya dubia, Ac. oblongata, Ac. polyandra, Aphanomyces bosminae, Ap. laevis, Dictychus monosporus, Pythium jirovecii, Py. undulatum, Saprolegnia ferax, S. parasitica, S. pseudocrustosa and Thraustotheca clavata. The human pathogens Aspergillus niger, Candida tropicalis and Catenophlyctis variabilis as well as plant pathogens Pythium butleri and Py. debaryanum were also found. Such phytosapro- phytes as Achlya klebsiana, Karlingia rosea, Nowakowskiella elegans, N. macrospora, Pythium akanense, Py. aquatile, Py. elongatum, Py. injlatum and Py. intermedium were relatively common. Most species of fungi and straminipilous organisms were found to grow in Dojlidy Pond (27), the fewest in Akcent Pond (14). The hydrochemical analysis of water showed that Dojlidy was the least burdened with organic matter, whereas Akcent was the most abundant in biogenic compounds.

The viriosphere: Which importance in the functioning and evolution of aquatic ecosystems (part II)?

Article

Jul 2009

Besides the lethal effect of viruses on the microbial community (typically the bacteria and the phytoplankton), the viral activity can affect significantly not only the structure of this community but also the cycling of carbon and other nutrients within aquatic ecosystems. Due to their activities, viruses could maintain the prokaryotic community diversity by lysing the most dominant populations then allowing the development of the minor groups. Also, viruses constitute the major driver of horizontal gene transfer between bacterial species or genus and therefore they could be the principal actor in the diversification of microbial communities. The viral lysis which induces the transformation of the biomass into dissolved organic matter pool could stimulate the microbial respiration and reduce the transfer of carbon to higher trophic levels as well as the sedimentation of organic particles towards the bottom. At last, aquatic viruses may generate an important interest for applied issues, typically the phagotherapy for aquaculture, even if an important effort remains to be done in the comprehension of the real efficiency of this therapy and the possible underlying resistance phenomena.

Substratum-Associated Microbiota

Abstract

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