Diversity, abundance, and potential activity of nitrifying and nitrate-reducing microbial assemblages in a subglacial ecosystem

Subglacial sediments sampled from beneath Robertson Glacier (RG), Alberta, Canada, were shown to harbor diverse assemblages of potential nitrifiers, nitrate reducers, and diazotrophs, as assessed by amoA, narG, and nifH gene biomarker diversity. Although archaeal amoA genes were detected, they were less abundant and less diverse than bacterial amoA, suggesting that bacteria are the predominant nitrifiers in RG sediments. Maximum nitrification and nitrate reduction rates in microcosms incubated at 4°C were 280 and 18.5 nmol of N per g of dry weight sediment per day, respectively, indicating the potential for these processes to occur in situ. Geochemical analyses of subglacial sediment pore waters and bulk subglacial meltwaters revealed low concentrations of inorganic and organic nitrogen compounds. These data, when coupled with a C/N atomic ratio of dissolved organic matter in subglacial pore waters of ~210, indicate that the sediment communities are N limited. This may reflect the combined biological activities of organic N mineralization, nitrification, and nitrate reduction. Despite evidence of N limitation and the detection of nifH, we were unable to detect biological nitrogen fixation activity in subglacial sediments. Collectively, the results presented here suggest a role for nitrification and nitrate reduction in sustaining microbial life in subglacial environments. Considering that ice currently covers 11% of the terrestrial landmass and has covered significantly greater portions of Earth at times in the past, the demonstration of nitrification and nitrate reduction in subglacial environments furthers our understanding of the potential for these environments to contribute to global biogeochemical cycles on glacial-interglacial timescales.     

Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment

The analysis of functional diversity and its dynamics in the environment is essential for understanding the microbial ecology and biogeochemistry of aquatic systems. Here we describe the development and optimization of a DNA microarray method for the detection and quantification of functional genes in the environment and report on their preliminary application to the study of the denitrification gene nirS in the Choptank River-Chesapeake Bay system. Intergenic and intragenic resolution constraints were determined by an oligonucleotide (70-mer) microarray approach. Complete signal separation was achieved when comparing unrelated genes within the nitrogen cycle (amoA, nifH, nirK, and nirS) and detecting different variants of the same gene, nirK, corresponding to organisms with two different physiological modes, ammonia oxidizers and denitrifying halobenzoate degraders. The limits of intragenic resolution were investigated with a microarray containing 64 nirS sequences comprising 14 cultured organisms and 50 clones obtained from the Choptank River in Maryland. The nirS oligonucleotides covered a range of sequence identities from approximately 40 to 100%. The threshold values for specificity were determined to be 87% sequence identity and a target-to-probe perfect match-to-mismatch binding free-energy ratio of 0.56. The lower detection limit was 10 pg of DNA (equivalent to approximately 10(7) copies) per target per microarray. Hybridization patterns on the microarray differed between sediment samples from two stations in the Choptank River, implying important differences in the composition of the denitirifer community along an environmental gradient of salinity, inorganic nitrogen, and dissolved organic carbon. This work establishes a useful set of design constraints (independent of the target gene) for the implementation of functional gene microarrays for environmental applications.     

Macrozoobenthic community structure in two Portuguese estuaries: Relationship with organic enrichment and nutrient gradients

The aim of this work consists in the study of the structural and functional aspects of the macrozoobenthic communities and their relationships with the organic enrichment and nutrient gradients in water and sediment. The study was carried out in two coastal ecosystems under strong anthropogenic pressure: the Sado estuary and the Aveiro Lagoon. Samples were collected at four stations between October 1994 and April 1995. The results obtained allowed us to state that spatial variability, both horizontal and vertical, was higher than the temporal variability. This was due to local hydrodynamism, organic load and granulometric structure of the sediment. Comparing the community structure at the different stations, it was possible to observe the existence of disturbance cases not directly related to organic enrichment gradients. The interpretation of the functional role of the macrozoobenthic communities at the water-sediment interface was based on the trophodynamic group classification. This approach allowed us to state that the sensitivity of different groups to organic enrichment, confirming the role of burrower subsurface-deposit feeders as opportunists associated with organic enrichment and, on the other hand, the influence of certain trophodynamic groups in the nutrient transfer processes, particularly the association between tube-builder omnivores and burrower carnivore and nitrate content in interstitial water.     

Seasonal and annual reoccurrence in betaproteobacterial ammonia-oxidizing bacterial population structure

Microbes exhibit remarkably high genetic diversity compared with plant and animal species. Many phylogenetically diverse but apparently functionally redundant microbial taxa are detectable within a cubic centimetre of mud or a millilitre of water, and the significance of this diversity, in terms of ecosystem function, has been difficult to understand. Thus it is not known whether temporal and spatial differences in microbial community composition are linked to particular environmental factors or might modulate ecosystem response to environmental change. Fifty-three water and sediment samples from upper and lower Chesapeake Bay were analysed in triplicate arrays to determine temporal and spatial patterns and relationships between ammonia-oxidizing bacterial (AOB) communities and environmental variables. Thirty-three water samples (three depths) collected during April, August and October, 2001-2004, from the oligohaline upper region of the Bay were analysed to investigate temporal patterns in archetype distribution. Using a combination of a non-weighted discrimination analysis and principal components analysis of community composition data obtained from functional gene microarrays, it was found that co-varying AOB assemblages reoccurred seasonally in concert with specific environmental conditions, potentially revealing patterns of niche differentiation. Among the most notable patterns were correlations of AOB archetypes with temperature, DON and ammonium concentrations. Different AOB archetypes were more prevalent at certain times of the year, e.g. some were more abundant every autumn and others every spring. This data set documents the successional return to an indigenous community following massive perturbation (hurricane induced flooding) as well as the seasonal reoccurrence of specific lineages, identified by key functional genes, associated with the biogeochemically important process nitrification.     

Springtime coupling between ice algal and phytoplankton assemblages in southeastern Hudson Bay,Canadian Arctic

Microalgal assemblages from the bottom ice, the ice-water interface and the water column were systematically sampled from April to June 1986, in southeastern Hudson Bay (Canadian Arctic). The taxonomic similarity between samples from the three environments was assessed using a clustering procedure. There were two groups that comprised samples from both the ice-water interface and the water column, while five other groups were made of samples originating from a single environment. Taxonomic compositions of the two mixed groups suggest two types of connexion between the ice-water interface and the water column, i.e. before the phytoplankton bloom, there was seeding of the water column by ice algae and, during ice melt, interfacial algae contributed to the water column communities that were otherwise typically phytoplankton. Overall, the phytoplankton community underwent a succession from pennate to centric diatoms. Sinking rates of algae from the ice-water interface were estimated using settling columns (SETCOL). The sinking rates increased seasonally (0.4–2.7 m d^–1), which enhanced accessibility of ice-algal cells to the pelagic grazers. Ice algae contributed to water column production as they became accessible to the pelagic grazers, and also by seeding the water column before the phytoplankton bloom.Contribution to the programs of GIROQ (Groupe interuniversitaire de recherches océanographiques du Québec) and of the Maurice Lamontagne Institute (Department of Fisheries and Oceans)     

Molecular characterization of diazotrophic and denitrifying bacteria associated with mangrove roots

An analysis of the molecular diversity of N(2) fixers and denitrifiers associated with mangrove roots was performed using terminal restriction length polymorphism (T-RFLP) of nifH (N(2) fixation) and nirS and nirK (denitrification), and the compositions and structures of these communities among three sites were compared. The number of operational taxonomic units (OTU) for nifH was higher than that for nirK or nirS at all three sites. Site 3, which had the highest organic matter and sand content in the rhizosphere sediment, as well as the lowest pore water oxygen concentration, had the highest nifH diversity. Principal component analysis of biogeochemical parameters identified soil texture, organic matter content, pore water oxygen concentration, and salinity as the main variables that differentiated the sites. Nonmetric multidimensional scaling (MDS) analyses of the T-RFLP data using the Bray-Curtis coefficient, group analyses, and pairwise comparisons between the sites clearly separated the OTU of site 3 from those of sites 1 and 2. For nirS, there were statistically significant differences in the composition of OTU among the sites, but the variability was less than for nifH. OTU defined on the basis of nirK were highly similar, and the three sites were not clearly separated on the basis of these sequences. The phylogenetic trees of nifH, nirK, and nirS showed that most of the cloned sequences were more similar to sequences from the rhizosphere isolates than to those from known strains or from other environments.     

Spatial and temporal distribution of two diazotrophic bacteria in the Chesapeake Bay

The aim of this study was to initiate autecological studies on uncultivated natural populations of diazotrophic bacteria by examining the distribution of specific diazotrophs in the Chesapeake Bay. By use of quantitative PCR, the abundance of two nifH sequences (907h22 and 912h4) was quantified in water samples collected along a transect from the head to the mouth of the Chesapeake Bay during cruises in April and October 2001 and 2002. Standard curves for the quantitative PCR assays demonstrated that the relationship between gene copies and cycle threshold was linear and highly reproducible from 1 to 10(7) gene copies. The maximum number of 907h22 gene copies detected was approximately 140 ml(-1) and the maximum number of 912h4 gene copies detected was approximately 340 ml(-1). Sequence 912h4 was most abundant at the mouth of the Chesapeake Bay, and in general, its abundance increased with increasing salinity, with the highest abundances observed in April 2002. Overall, the 907h22 phylotype was most abundant at the mid-bay station. Additionally, 907h22 was most abundant in the April samples from the mid-bay and mouth of the Chesapeake Bay. Despite the fact that the Chesapeake Bay is rarely nitrogen limited, our results show that individual nitrogen-fixing bacteria have distinct nonrandom spatial and seasonal distributions in the Chesapeake Bay and are either distributed by specific physical processes or adapted to different environmental niches.     

亚热带河口陆基养虾塘水体溶解性碳浓度及沉积物-水界面碳通量时空动态特征

以福建闽江和九龙江河口陆基养虾塘为研究对象,通过野外原位观测和室内模拟培养实验,开展了河口陆基养虾塘养殖期间水体溶解性有机碳(DOC)和溶解性无机碳(DIC)及养虾塘沉积物-水界面碳交换通量变化特征的研究。结果表明:时间变化上,养虾塘水体溶解性碳浓度及沉积物-水界面碳通量在闽江河口呈现8月中旬10月中旬6月中旬的特征,在九龙江河口表现为随养殖阶段推移而增加的趋势;空间变化上,闽江河口养虾塘水体溶解性碳浓度及沉积物-水界面碳通量显著高于九龙江河口;沉积物释放溶解性碳速率与水体溶解性碳浓度呈现显著正相关关系,沉积物碳释放过程是引起养虾塘水体溶解性碳浓度时空变化的重要因素。表明河口区水产养虾塘碳循环研究时需考虑不同形态碳生物地球化学循环的时空差异性。     

BENTHIC DIATOM AUTECOLOGY AND INFERENCE MODEL DEVELOPMENT FROM THE CANADIAN HIGH ARCTIC ARCHIPELAGO1

Diatom assemblages were analyzed from 64 lakes and ponds from Alert, Ellesmere Island and Mould Bay, Prince Patrick Island in the Canadian High Arctic Archipelago. Diverse water chemistry conditions and diatom communities were present in these sites. Small benthic taxa typically dominated diatom communities; however, assemblages were markedly different between Alert and Mould Bay sites in response to disparate water chemistry characteristics in the two regions. The most abundant taxa belonged to the genera Navicula, Cymbella, Achnanthes, Nitzschia, and Pinnularia. Canonical correspondence analysis indicated that pH, specific conductivity, dissolved organic carbon, and total phosphorus were the most important limnological variables in determining species composition. Diatom inference models were developed for pH, specific conductivity, and dissolved organic carbon using weighted averaging and weighted averaging partial least squares techniques; these had root mean square error of prediction/r²_boot values of 0.40/0.77, 0.28/0.70, and 0.24/0.55, respectively. These models are applicable to sites with large ranges of taxonomic and limnological variation and will allow the reconstruction of past changes of climate‐related limnological parameters from biostratigraphic records in future paleolimnological studies.     

Nitrogen-fixing phylotypes of Chesapeake Bay and Neuse River estuary sediments

Sediments often exhibit low rates of nitrogen fixation, despite the presence of elevated concentrations of inorganic nitrogen. The organisms that potentially fix nitrogen in sediments have not previously been identified. Amplification of nifH genes with degenerate primers was used to assess the diversity of diazotrophs in two distinct sediment systems, anoxic muds of Chesapeake Bay and shallow surficial sediments of the Neuse River. Phylogenetic analysis revealed that sequences obtained from mid-Chesapeake Bay, which receive high organic loading and are highly reducing, clustered closely with each other and with known anaerobic microorganisms, suggesting a low abundance of aerobic or facultative diazotrophs in these sediments. Sulfate reduction dominates in the surface, but methanogenesis becomes more important with depth. A thin (<1 cm) oxidized layer is present only in the spring. No archaeal nifH sequences were obtained from Chesapeake Bay. Sequences of nifH amplified from surficial sediments of the Neuse River were distant from Chesapeake Bay sequences and included nif phylotypes related to sequences previously reported from marine mats and the Spartina rhizosphere. Differences in environmental site characteristics appear to select for different types of sediment diazotrophs, which is reflected in the phylogenetic composition of amplified nifH sequences.     

Interannual dynamics of viriobenthos abundance and morphological diversity in Chesapeake Bay sediments

Despite significant implications of viral activity in sediment ecosystems, there are limited data describing how sediment viral assemblages respond to broader ecosystem changes. To document this, the spatial and temporal dynamics of viral and bacterial abundance (BA) and changes in the morphological distribution of viruses were examined within three salinity regions over 2 years. Viral abundances (VA) ranged from 0.2 to 17 × 10(10) viruses mL(-1) sediment while direct bacterial counts ranged from 3.8 to 37 × 10(8) cells mL(-1) sediment. Peaks and valleys in the abundance of extracted viruses and bacteria from surface sediments occurred simultaneously, with lows in February 2004 and highs in April 2003. Across all samples, viral and BA were positively correlated (P < 0.001). Vertical profiles showed a decrease in viral and BA with depth in sediments. Based on transmission electron microscopy results, viruses with diminutive capsids (20-50 nm) and from the Myoviridae and Podoviridae viral family types were dominant within surface sediments. The most morphologically diverse viral assemblages occurred in autumn samples from the sandy, polyhaline station and spring samples from the mesohaline station. Seasonal changes showed an average 72% decrease in VA from spring to winter. These observations support the view that viriobenthos assemblages are responsive to seasonal environmental changes and that viral processes have significant implications for the biogeochemical processes mediated by bacterial communities within Bay sediments.     

DISTRIBUTION OF INTERTIDAL DIATOMS ASSOCIATED WITH SEDIMENTS IN YAQUINA ESTUARY,OREGON1,2

Sediment samples and environmental data were collected from November 1973 to August 1974 to analyze the distribution of sediment-associated diatom assemblages relative to vertical, horizontal, and seasonal gradients in Yaquina Estuary, Oregon. The distribution of diatoms was regulated primarily by mean salinity and characteristics of the sediment, i.e., mean sediment size and percentage of organic carbon. Prominent taxa in the river above Yaquina Bay exhibited overlapping distributions along the salinity gradient to a location in brackish water where the mean salinity was approximately 5%_o. At this salinity, a relatively sharp discontinuity in the diatom flora existed which appeared to represent the biochemical and biophysical mechanisms involved in the osmotic regulation of fresh- and brackish-water diatoms. Relatively large disparities m the structure of diatom assemblages were found within relatively small areas of Yaquina Bay. These differences were attributed to properties of the sediment. Differences in diatom assemblages relative to variations in light intensity, water temperature and exposure to intertidal emergence were not apparent from the analysis of field data.     

Land forcing controls pelagic-benthic coupling in Adelie Cove (Terra Nova Bay, Ross Sea)

Benthic-pelagic coupling processes were studied in Adelie Cove, a small 70-m deep V-shaped bay, located on the coast of Terra Nova Bay (Ross Sea). This cove is set apart from the open sea by a 12- to 15-m deep sill. Samplings were carried out over 20 days in summer 1997/1998 in the water column, in the sediment and in material collected from the sea-bottom interface by means of a sediment trap. Benthic communities were studied mainly using ROV video tapes. The complex and peculiar interactions between physical, chemical and biological processes, both in the water column and in the sediments, were tightly linked to a katabatic wind pattern, which is the main constraint in water mass circulation. A clear evolution in organic matter distribution and composition was observed. These processes led to a high build-up of materials in the sediments in the deepest part of the cove, which favoured deposit-feeding species and largely contributed to the organic enrichment of the sediments.     

AN INVESTIGATION OF DISTRIBUTIONAL PATTERNS IN THE DIATOM FLORA OF NETARTS BAY,OREGON, BY CORRESPONDENCE ANALYSIS1

Distributional patterns in assemblages of epiphytic and sediment-associated diatoms were investigated in Netarts Bay, Oregon. The method of reciprocal averaging revealed a floristic discontinuity between the epiphytic and sediment samples in ordination space. The basis for this discontinuity was the presence of a large number of sediment-associated taxa that were either very rare or not observed in the epiphytic samples. Within the sediment samples, the diatom flora formed a distributional continuum which had relatively high correlations with mean grain size, a sediment sorting coefficient, and the organic matter content of the sediment. A comparison of the flora in Netarts Bay with floras in other Oregon estuaries indicates that epiphytic, epilithic, and sediment-associated diatom assemblages do not exhibit conspicuous latitudinal changes along the coast of Oregon, and that many of the same taxa can be expected to occur in samples from comparable habitats in estuaries throughout the temperate regions of the world.     

Climate drivers of diatom distribution in shallow subarctic lakes

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Sedimentary microbial community dynamics in a regulated stream: East Fork of the Little Miami River,Ohio

A field study was conducted in the Lower East Fork of the Little Miami River, a regulated stream in Clermont county, Ohio, to determine how changes in streamflow, water temperature and photo-period affect sediment microbial community structure. Surface sediment cores were collected from sampling stations spanning 60 river kilometers three to four times per year between October 1996 and October 1999. During the final year of the field study, water temperature, water depth, conductivity, total suspended solids, dissolved organic carbon, instantaneous streamflow velocity, sediment grain size and sediment organic matter were determined. Total microbial biomass was measured using the phospholipid phosphate technique (PLP) and ranged between 2 and 134 nmol PLP * g(-1) dry weight sediment with a mean of 25 nmol PLP * g(-1). Microbial community structure was determined using the phospholipid fatty acid analysis and indicated seasonal shifts in sedimentary microbial community composition. January to June sedimentary microbial biomass was predominately prokaryotic (60% +/- 2), whereas microeukaryotes dominated samples collected during the late summer (55% +/- 2.4) and fall (60% +/- 2). These changes were correlated with stream discharge and water temperature. Microbial community structure varied spatially about a reservoir with prokaryotic biomass dominant at upstream stations and eukaryotic biomass dominant at downstream stations. These findings reveal that sedimentary microbial communities in streams are dynamic responding to the seasonal variation of environmental factors.     

Distribution of viral abundance in the reef environment of Key Largo, Florida.

The distribution of viral and microbial abundance in the Key Largo, Fla., reef environment was measured. Viral abundance was measured by transmission electron microscope direct counts and plaque titer on specific bacterial hosts in water and sediment samples from Florida Bay (Blackwater Sound) and along a transect from Key Largo to the outer edge of the reef tract in Key Largo Sanctuary. Water column viral direct counts were highest in Blackwater Sound of Florida Bay (1.2 x 10(7) viruses per ml), decreased to the shelf break (1.7 x 10(6) viruses per ml), and were inversely correlated with salinity (r = -0.97). Viral direct counts in sediment samples ranged from 1.35 x 10(8) to 5.3 x 10(8)/cm(3) of sediment and averaged nearly 2 orders of magnitude greater than counts in the water column. Viral direct counts (both sediment and water column measurements) exceeded plaque titers on marine bacterial hosts (Vibrio natriegens and others) by 7 to 8 orders of magnitude. Water column viral abundance did not correlate with bacterial direct counts or chlorophyll a measurements, and sediment viral parameters did not correlate with water column microbial, viral, or salinity data. Coliphage, which are indicators of fecal pollution, were detected in two water column samples and most sediment samples, yet their concentrations were relatively low (<2 to 15/liter for water column samples, and <2 to 108/cm(3) of sediment). Our findings indicate that viruses are abundant in the Key Largo environment, particularly on the Florida Bay side of Key Largo, and that processes governing their distribution in the water column (i.e., salinity and freshwater input) are independent of those governing their distribution in the sediment environment.     

Estimates of bacterial productivity in marine sediments and water from a temperate saltmarsh lagoon

Tritiated thymidine incorporation (TTI) into DNA was used to estimate bacterial productivity in sediment and water samples from two sites in Langebaan Lagoon, South Africa. Routine analysis of isotope dilution showed seasonal variations of approximately threefold in the thymidine precursor pool sizes for bacterial assemblages from each site. Dual label incorporation of [³H]-thymidine and ¹⁴C-leucine into DNA and protein, respectively, showed that pelagic but not sediment assemblages were in a balanced state of growth during TTI. This is the first report of dual label measurements of bacterial production in sediments. Sediments supported bacterial productivities that exceeded those in the water column by factors from five- to 950-fold, whereas bacterial abundance supported by sediments exceeded that in the water column by more than 3 orders of magnitude. Estimates of bacterial productivities in sediments were coincident with levels of organic content in sediments, but not with bacterial abundance. Measurements of TTI activity for 5 different benthic microhabitats at one lagoon site showed highest activity associated with seagrass beds (2.11 ± 0.84 nmol thymidine hours^–1 g-1 dry weight), whereas activities decreased with depth (0.46 ± 0.21 nmol thymidine hours^–1 g^–I dry weight) below sediment surface.Offprint requests to: B. J. Tibbles.     

Seasonal variations of Microcystis populations in sediments of Lake Biwa, Japan

Seasonal variations of colony numbers of Microcystis aeruginosa(Kütz.) Kütz. and M. wesenbergii(Komárek) Komárek in N. V. Kondrat. in sediments of Lake Biwa were investigated over a period of 1 year. At two stations located in the shallow South Basin of Lake Biwa (ca. 4 m water depth), the colony number of Microcystisfluctuated seasonally. The number had a tendency to gradually decrease from winter to early summer, while it increased through mid-summer and autumn. Since the Microcystispopulation in sediment was rather small, intensive growth and accumulation in the water column should be important for the formation of Microcystisblooms in Lake Biwa. Microcystiscolonies in the sediment samples after June were observed to be floating in a counting chamber under a microscope. The observation suggests that the recruitment of Microcystis colonies into the water column mostly occurs in early summer. The number of Microcystiscolonies in the deep North Basin of Lake Biwa (70 – 90 m water depth) was larger than in the South Basin. Because the seasonal variation of colony numbers was not observed in the North Basin, and Microcystiscells do not have gas vesicles, these colonies will not return into the water column. The colonies isolated from the sediment of the North Basin were able to grow in cultured conditions, in the same way as those from the sediment of the South Basin. Therefore, Microcystiscolonies may survive for a long time under stable conditions of low temperature (ca. 8 °C) and darkness, in the sediment of the deep North Basin, accumulating gradually each year.