Microenvironments and microbial community structure in sediments

The aim of this study was to explore the potential of a combined chemical and microbiological approach as part of a study of organic carbon oxidation processes in sediments. An assessment of microbiological diversity using molecular techniques was carried out in combination with high resolution chemical measurements at the sediment-water interface of a coastal lagoon affected by eutrophication in autumn 2000. There was a 0.2 mm overlap between the O2 and H2S profiles. pH showed a maximum just above the sediment-water interface coinciding with an oxygen maximum, suggesting photosynthetic activity, and a minimum coinciding with the O2-H2S interface. The redox potential was high in bottom water and surface sediment, reflecting the presence of oxygen and oxides, and reached low values after a step-wise decrease at -18 mm. Reduction of Fe occurred within the biofilm at the O2-H2S interface and was mostly due to reduction by H2S. The elevated concentrations of dissolved Mn in the oxic water may have been caused either by in situ production within organic aggregates or lateral water flow from sites nearby at which Mn2+ diffuses out of the sediment. Sequences related to sulphur chemolitotrophs were retrieved from the biofilm samples, which is consistent with the small overlap between O2 and H2S observed in this biofilm. Although the resolution of techniques used was different, sequencing results were consistent with chemical data in delineating the same horizons according to redox, pH or ecological properties.     

Short-term stability of the microbial community structure in a maritime Antarctic lake

. Spatial and temporal changes in the microbial community structure in a maritime Antarctic freshwater lake were investigated over a single day/night cycle in December 1999. The community structure of key microbial planktonic groups varied with depth and this was related to both physical and chemical stratification. However, in most cases, the community structure observed at specific depths did not change over the time period studied. These results suggested short-term stability in community structure, with only some minor effects of the diel changes in irradiance on the vertical distribution of planktonic organisms. This is in marked contrast to medium- and long-term studies, which show significant changes in microbial community structure with both time and depth.     

青藏高原湖泊沉积物中有机碳组分构成及其对微生物群落结构的影响

【目的】探究湖泊沉积物中有机碳组分构成及其对湖泊微生物群落结构的影响。【方法】本研究采集了青藏高原29个湖泊共81个沉积物样品,通过硫酸水解法分析样品中易降解和难降解有机碳含量及其与环境变量之间的相关性;同时使用高通量测序技术分析样品中原核微生物和真菌群落的多样性和组成及其与易降解和难降解有机碳含量的相关关系。【结果】本研究的青藏高原湖泊沉积物中易降解有机碳Ⅰ(labile organic carbon Ⅰ, LOCⅠ)、易降解有机碳Ⅱ(labile organic carbon Ⅱ, LOCⅡ)和难降解有机碳(recalcitrant organic carbon, ROC)的含量分别为0.03–29.62 mg/g、0.02–23.38 mg/g和0.64–75.72 mg/g,ROC是沉积物有机碳的主要组分(占比为54.97%±19.50%)。LOCⅠ含量与海拔、总氮、总磷、钙离子、活性钙和活性铁含量显著相关(P<0.05);LOCⅡ含量与总氮、钙离子和活性钙含量显著相关;而ROC含量与海拔、总氮、总磷、钙离子和活性钙含量显著相关。其中,钙离子和活性钙的浓度与3种有机碳组分...     

Quinone profiles in lake sediments: Implications for microbial diversity and community structures

Microbial quinone compositions of sediment mud samples from five different lakes in Japan were studied by spectrochromatography and mass spectrometry. The total quinone content of these samples ranged from 1.97 to 18.0 nmol/g dry weight of sediment, of which a combined fraction of ubiquinones and menaquinones accounted for 42 to 74%. The remaining fraction (26 to 58%) consisted of the photosynthetic quinones, plastoquinones and phylloquinone. The sediment samples produced PQ-9 or Q-8 as the most abundant quinone type regardless of their geographic locations and depths. These results indicate that oxygenic phototrophic microorganisms and Q-8-containing proteobacteria constituted major parts of microbial populations in the lake sediment. In the surface water of the same sampling sites, plastoquinones and phylloquinone occurred in much higher proportions. These findings suggested that the high abundance of oxygenic phototrophs in the sediment muds resulted from their constant movement or sedimentation from the surface water. Numerical analyses of the quinone profiles showed that the microbial communities of the sediment were diverse and different in different lakes but similar to each other in the diversity of bioenergetic modes. Three physiological groups of microbes showing ubiquinone-mediated aerobic respiration, oxygenic photosynthesis, and menaquinone-associated respiration were suggested to inhabit the lake sediments in balance.     

基于PCR-DGGE技术的红树林区微生物群落结构

【目的】为了解红树林沉积物中细菌的群落结构特征。【方法】应用PCR-DGGE技术对福建浮宫红树林的16个采样站位样品细菌的群落结构进行了研究。根据DGGE指纹图谱,对它们的遗传多样性进行了分析。【结果】各站位样品细菌多样性指数(H)、丰度(S)和均匀度(EH)均有所不同,这些差异与它们所处站位的不同有关,红树林区细菌多样性高于非红树林区细菌多样性。对不同站位细菌群落相似性分析,它们的相似性系数也存在一定的规律,同一断面的细菌群落结构相近性较高。对DGGE的优势条带序列分析,同源性最高的微生物分别属于变形菌门(Proteobacteria)、酸菌门(Acidobacteria)和绿菌门(Chlorobi),它们均为未培养微生物,分别来自于河口海岸沉积物。【结论】应用PCR-DGGE技术更能客观地反映红树林沉积物中真实的细菌群落结构信息。另外,研究也表明红树林区微生物多样性丰富,在红树林区研究开发未知微生物资源具有巨大的潜力。     

The microbial community structure in petroleum-contaminated sediments corresponds to geophysical signatures

The interdependence between geoelectrical signatures at underground petroleum plumes and the structures of subsurface microbial communities was investigated. For sediments contaminated with light non-aqueous-phase liquids, anomalous high conductivity values have been observed. Vertical changes in the geoelectrical properties of the sediments were concomitant with significant changes in the microbial community structures as determined by the construction and evaluation of 16S rRNA gene libraries. DNA sequencing of clones from four 16S rRNA gene libraries from different depths of a contaminated field site and two libraries from an uncontaminated background site revealed spatial heterogeneity in the microbial community structures. Correspondence analysis showed that the presence of distinct microbial populations, including the various hydrocarbon-degrading, syntrophic, sulfate-reducing, and dissimilatory-iron-reducing populations, was a contributing factor to the elevated geoelectrical measurements. Thus, through their growth and metabolic activities, microbial populations that have adapted to the use of petroleum as a carbon source can strongly influence their geophysical surroundings. Since changes in the geophysical properties of contaminated sediments parallel changes in the microbial community compositions, it is suggested that geoelectrical measurements can be a cost-efficient tool to guide microbiological sampling for microbial ecology studies during the monitoring of natural or engineered bioremediation processes.     

Alarm communication networks as a driver of community structure in African savannah herbivores

Social information networks have the potential to shape the spatial structure of ecological communities by promoting the formation of mixed‐species groups. However, what actually drives social affinity between species in the wild will depend on the characteristics of the species available to group. Here we first present an agent‐based model that predicts trait‐related survival benefits from mixed‐species group formation in a multi‐species community and we then test the model predictions in a community‐wide field study of African savannah herbivores using multi‐layered network analysis. We reveal benefits from information transfer about predators as a key determinant of mixed‐species group formation, and that dilution benefits alone are not enough to explain patterns in interspecific sociality. The findings highlight the limitations of classical ecological approaches focusing only on direct trophic interactions when analysing community structure and suggest that declines in species occupying central social network positions, such as key informants, can have significant repercussions throughout communities.     

Seasonal microbial activity in Antarctic freshwater lake sediments

Summary Seasonal fluctuations in population numbers and activity were monitored in bottom sediments of oligotrophic Moss Lake, mesotrophic Heywood Lake and eutrophic Amos Lake on Signy Island, South Orkney Islands, during 1976–78. Heywood and Amos Lakes became anoxic under winter ice cover (8–10 months) and significant populations of facultatively anaerobic heterotrophs and sulphate-reducing bacteria developed. In contrast, Moss Lake surface sediments never became anoxic and anaerobic bacteria were virtually absent. Direct microscopic counts and viable plate counts fluctuated relatively little in Moss Lake throughout the study period, whereas distinct seasonality was observed in the more enriched lake systems. Similarly, measurements of oxygen consumption and dark ¹⁴CO₂ uptake by mud cores indicated no obvious seasonal fluctuations in Moss Lake data, in contrast to the marked seasonal pattern observed in data from the other lakes. In these latter systems, oxygen uptake rates were highest in summer (c. 400 mg O₂ m^-2 d^-1) and virtually undetectable in winter. Comparison of oxygen uptake with oxygen concentration and temperature revealed differences, between lakes, in uptake response to oxygen concentration, whereas uptake response to temperature did not differ significantly between lakes. Chemosynthetic production in the Signy Island lake sediments was in the range 1.6–35.3 g C m^-2 (mud surface) d^-1 with highest values recorded in Amos Lake under winter ice cover and anoxic conditions. The findings from this and earlier studies of the three lakes have been assembled to indicate the relative importance of green plants and bacteria to the carbon cycle in these permanently cold systems.     

Influence of TNT transformation on microbial community structure in four different lake microcosms

After World War II, large amounts of obsolete ammunition were dumped in various lakes in Sweden. Trinitrotoluene, TNT, was one of the main components of the dumped explosives. In this study, four different lake microcosms originating from lakes where relatively large amounts of ammunition were dumped were used to mimic the effect of TNT release on the natural microbial community. Increased microbial growth was found in lake microcosms amended with TNT. However, negligible mineralization of TNT was detected, suggesting that TNT was not utilized as a carbon source, but as a nitrogen source. Random amplified polymorphic DNA (RAPD) analysis indicated that the TNT induced no significant differences in microbial community composition and therefore, no major changes in natural selection, despite the increased microbial growth in the presence of the compound. More than 95% of the added TNT bound irreversibly to the sediments, possibly as a result of microbial transformation to reactive metabolites that subsequently bound covalently to components of the sediment. The results, taken together, suggest that no permanent change in the microbial ecology occurred as a result of the TNT amendment. This was probably due partly to the transient exposure of the microbial communities to the TNT before it became irreversibly bound to the sediment, and partly to the fact that TNT was not a primary growth substrate that strongly affects natural selection.     

Eutrophication as a driver of r‐selection traits in a freshwater fish

This study tested whether eutrophication could influence life‐history traits of a cyprinid, Chanodichthys erythropterus, in 10 Chinese lakes. Using the von Bertalanffy growth model, the asymptotic length (L_∞) and the growth performance index (I_GRO) were significantly affected by eutrophication. The gonado‐somatic index (I_G) and relative fecundity (F_R) were significantly lower in mesotrophic lakes than in eutrophic and hypertrophic lakes. These results indicate that increasing eutrophication affects the life‐history tactics of a freshwater fish.     

Variation in microbial biomass and community structure in sediments of eutrophic bays as determined by phospholipid ester-linked Fatty acids

[This corrects the article on p. 562 in vol. 58.].     

Qualitative importance of the microbial loop and plankton community structure in a eutrophic lake during a bloom of cyanobacteria

Plankton community structure and major pools and fluxes of carbon were observed before and after culmination of a bloom of cyanobacteria in eutrophic Frederiksborg Slotssø, Denmark. Biomass changes of heterotrophic nanoflagellates, ciliates, microzooplankton (50 to 140 μm), and macrozooplankton (larger than 140 μm) were compared to phytoplankton and bacterial production as well as micro- and macrozooplankton ingestion rates of phytoplankton and bacteria. The carbon budget was used as a means to examine causal relationships in the plankton community. Phytoplankton biomass decreased and algae smaller than 20 μm replacedAphanizomenon after the culmination of cyanobacteria. Bacterial net production peaked shortly after the culmination of the bloom (510 μg C liter^?1 d^?1 and decreased thereafter to a level of approximately 124 μg C liter^?1 d^?1. Phytoplankton extracellular release of organic carbon accounted for only 4–9% of bacterial carbon demand. Cyclopoid copepods and small-sized cladocerans started to grow after the culmination, but food limitation probably controlled the biomass after the collapse of the bloom. Grazing of micro- and macrozooplankton were estimated from in situ experiments using labeled bacteria and algae. Macrozooplankton grazed 22% of bacterial net production during the bloom and 86% after the bloom, while microzooplankton (nauplii, rotifers and ciliates larger than 50 μm) ingested low amounts of bacteria and removed 10–16% of bacterial carbon. Both macro-and microzooplankton grazed algae smaller than 20 μm, although they did not control algal biomass. From calculated clearance rates it was found that heterotrophic nanoflagellates (40–440 ml^?1) grazed 3–4% of the bacterial production, while ciliates smaller than 50 μm removed 19–39% of bacterial production, supporting the idea that ciliates are an important link between bacteria and higher trophic levels. During and after the bloom ofAphanizomenon, major fluxes of carbon between bacteria, ciliates and crustaceans were observed, and heterotrophic nanoflagellates played a minor role in the pelagic food web.     

A meta-analysis of benthic rotifer community structure as a function of lake trophic state

Aquatic Ecology - Our understanding of the ecological drivers that control community structure of benthic rotifers is poorly known. By reviewing 21 papers on freshwater benthic rotifers we compiled...     

Experimental manipulations of microbial food web interactions in a humic lake: shifting biological drivers of bacterial community structure

A previous multiyear study observed correlations between bacterioplankton community composition (BCC) and abundance and the dynamics of phytoplankton populations and bacterivorous grazers in a humic lake. These observations generated hypotheses about the importance of trophic interactions (both top-down and bottom-up) for structuring bacterial communities in this lake, which were tested using two multifactorial food web manipulation experiments that separately manipulated the intensity of grazing and the composition of the phytoplankton community. Our results, combined with field observations, suggest that a hierarchy of drivers structures bacterial communities in this lake. While other studies have noted links between aggregate measures of phytoplankton and bacterioplankton communities, we demonstrate here correlations between succession of phytoplankton assemblages and BCC as assessed by automated ribosomal intergenic spacer analysis (ARISA). We used a novel approach linking community ARISA data to phylogenetic assignments from sequence analysis of 16S rRNA gene clone libraries to examine the responses of specific bacterial phylotypes to the experimental manipulations. The synchronous dynamics of these populations suggests that primary producers may mediate BCC and diversity through labile organic matter production, which evolves in quality and quantity during phytoplankton succession. Superimposed on this resource-mediated control of BCC are brief periods of intense bacterivory that impact bacterial abundance and composition.     

Chaoborus predation and zooplankton community structure in a rotifer-dominated lake

During summer, Chaoborus punctipennis larval densities in the water column of fishless, eutrophic Triangle Lake become very high, and coincidently, the spined loricate rotifer Kelfcottia bostoniensis becomes the dominant zooplankter. Research was done to test the hypothesis that selective predation by Chaoborus on soft-bodied rotifers controls species dominance in the mid-summer zooplankton of this lake. In situ predation experiments showed positive selection by Chaoborus for the soft-bodied Synchaeta oblonga, negative selection for K. bostoniensis, and intermediate selection for Polyarthra vulgaris, a species with rapid escape tactics. However, during a 21 day in situ mesocosm experiment, zooplankton dominance and succession in Chaoborus-free enclosures was identical to that in enclosures with Chaoborus at lake density. Despite the selective predation, Chaoborus larvae may not exert significant top-down control on rotifers, whose intense reproductive output during mid-summer in temperate eutrophic lakes results in new individuals at rates that exceed predatory losses.     

Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community

Microbial community succession was examined over a two-year period using spatially and temporally coordinated water chemistry measurements, metagenomic sequencing, phylogenetic binning and de novo metagenomic assembly in the extreme hypersaline habitat of Lake Tyrrell, Victoria, Australia. Relative abundances of Haloquadratum-related sequences were positively correlated with co-varying concentrations of potassium, magnesium and sulfate, but not sodium, chloride or calcium ions, while relative abundances of Halorubrum, Haloarcula, Halonotius, Halobaculum and Salinibacter-related sequences correlated negatively with Haloquadratum and these same ionic factors. Nanohaloarchaea and Halorhabdus-related sequence abundances were inversely correlated with each other, but not other taxonomic groups. These data, along with predicted gene functions from nearly-complete assembled population metagenomes, suggest different ecological phenotypes for Nanohaloarchaea and Halorhabdus-related strains versus other community members. Nucleotide percent G+C compositions were consistently lower in community metagenomic reads from summer versus winter samples. The same seasonal G+C trends were observed within taxonomically binned read subsets from each of seven different genus-level archaeal groups. Relative seasonal abundances were also linked to percent G+C for assembled population genomes. Together, these data suggest that extreme ionic conditions may exert selective pressure on archaeal populations at the level of genomic nucleotide composition, thus contributing to seasonal successional processes. Despite the unavailability of cultured representatives for most of the organisms identified in this study, effective coordination of physical and biological measurements has enabled discovery and quantification of unexpected taxon-specific, environmentally mediated factors influencing microbial community structure.     

Freeze coring as a method of collecting unconsolidated lake sediments

The paper describes a method of collecting unconsolidated lake sediment by freezing the in situ sediment to the outer surface of an aluminium tube. This prevents any disturbance and disruption of the stratigraphy which would otherwise occur because of the release of dissolved gas resulting from the pressure and temperature change on bringing the sediment to the surface. Sampling methods were tested on the laminated sediments of Lake Barrine, North Queensland.     

Microbial community structure and biogeochemistry of Miocene subsurface sediments: implications for long-term microbial survival

Thirty closely spaced cores were obtained from Miocene-aged fluvial, lacustrine and palaeosol subsurface sediments ranging in depth from 173 to 197 m at a site in south-central Washington to investigate the size and composition of the microbial community in relation to sediment geochemical and geophysical properties. Total phospholipid fatty acid (PLFA) analysis indicated that the greatest concentrations of microbial bio-mass were in low-permeability lacustrine sediments that also contained high concentrations of organic carbon. Community structure, based on lipid analyses and on in situ hybridization of bacterial cells with 16S RNA-directed DNA probes, also revealed the presence of metabolically active bacteria that respire sulphate and/or Fe(III) in the lacustrine sediments. Concentrations of pore water sulphate were low (4–8 mg/L) and HCI-extractable Fe was predominantly Fe(II) in the same samples where total biomass and organic carbon were highest. The low hydraulic conductivity (10^-6 to < 10^-9 cm/s) of these sediments has likely contributed to the long term maintenance of both bacteria and organic carbon by limiting the supply of soluble electron acceptors for microbial respiration. These results suggest that the current subsurface microbial population was derived from organisms that were present during lake sedimentation = 6–8 million years ago.     

Seasonal dynamics of the planktonic microbial community in a maritime Antarctic lake undergoing eutrophication

The abundance, biomass and community structure of phytoplankton,bacterioplankton and protozooplankton in a maritime Antarcticlake were determined at approximately monthly intervals fromDecember 1994 to February 1996 and compared with data from earlierstudies. Heywood Lake has become significantly eutrophic duringthe last three decades because of excreta from the expandingfur seal population in its catchment. Marked seasonal variationsin the abundance, composition and productivity of biota werecorrelated with the seasonality of both physical factors andnutrient levels. Protozooplankton were abundant, diverse andusually dominated by heterotrophic nanoflagellates (HNF), withHNF abundance peaking at 2.35 x 10⁷ l^–1 in summer. Highnumbers of naked amoebae were sometimes present, reaching amaximum of 4.8 x 10³ l^–1 in March. An estimated 89 speciesof protozoa were observed during the study, indicating substantiallymore diversity than is found in continental Antarctic lakes.Diversity was highest in spring and lowest in winter, when theentire water column became anoxic and the plankton were dominatedby bacteria and a few species of relatively large anaerobicflagellates. The current status of the lake is compared withdata for continental Antarctic and lower latitude lakes. Earlierstudies of biota and physical/chemical parameters in HeywoodLake are used to examine the effects of eutrophication overthree decades. Observed changes include increased microbialabundance and changes in both community structure and seasonalpatterns.