Distinct Community Structure Research Articles

Spatial and seasonal variations in mercury methylation and microbial community structure in a historic mercury mining area, Yolo County, California

The relationships between soil parent lithology, nutrient concentrations, microbial biomass and community structure were evaluated in soils from a small watershed impacted by historic Hg mining. Upland and wetland soils, stream sediments and tailings were collected and analyzed for nutrients (DOC, SO 4 =, NO 3 −), Hg, MeHg, and phospholipid fatty acids (PLFA). Stream sediment was derived from serpentinite, siltstone, volcanic rocks and mineralized serpentine with cinnabar, metacinnabar and other Hg phases. Soils from different parent materials had distinct PLFA biomass and community structures that are related to nutrient concentrations and toxicity effects of trace metals including Hg. The formation of MeHg appears to be most strongly linked to soil moisture, which in turn has a correlative relationship with PLFA biomass in wetland soils. The greatest concentrations of MeHg (> 0.5 ng g − 1 MeHg) were measured in wetland soils and soil with a volcanic parent (9.5–37 µg g − 1 Hg). Mercury methylation was associated with sulfate-reducing bacteria, including Desulfobacter sp. and Desulfovibrio sp., although these organisms are not exclusively responsible for Hg methylation. Statistical models of the data demonstrated that soil microbial communities varied more with soil type than with season.

Molecular methods to detect and monitor dissimilatory arsenate-respiring bacteria (DARB) in sediments

Dissimilatory arsenate-respiring bacteria (DARB) reduce arsenate to arsenite and may play a significant role in arsenic mobilization in aquifers and anoxic sediments. Many studies have been conducted with pure cultures of DARB to understand their involvement in arsenic contamination. However, few studies have examined uncultured DARB in the environment. In order to investigate uncultured DARB in anoxic sediments, genes encoding arsenate respiratory reductases (arr) were targeted as a genetic marker. Degenerate primers for the alpha-subunit of arr genes were designed and used with PCR amplification to detect uncultured DARB in the sediments collected from three stations (upper, mid and lower bay) in the Chesapeake Bay. Phylogenetic analysis of putative arrA genes revealed the diversity of DARB with distinct community structures at each of the three stations. Arsenate reduction in sediment communities was confirmed using enrichment cultures established with sediment samples from the upper bay. In addition, terminal restriction fragment length polymorphism analysis of the putative arrA genes showed changes in the community structure of DARB in the enrichment cultures while reducing arsenate. This was also confirmed by cloning and sequence analysis of the arrA genes obtained from the enrichment cultures. Thus, we were able to detect diverse uncultured DARB in sediments, as well as to describe changes in DARB community structure during arsenic reduction in anoxic environments.

Utilisation of introduced Brazilian pastures ecosystems by native dung beetles: diversity patterns and resource use

Abstract. Cattle pastures dominated by introduced grasses are a characteristic component of many tropical landscapes in Brazil, yet little information is available concerning the insect communities that inhabit these novel ecosystems. Dung beetles are a conspicuous element of pasture insect communities, and make a significant contribution to dung decomposition, parasitic fly control, and soil bioturbation. We sampled dung beetle assemblages in twelve introduced pastures near Viçosa, Minas Gerais, Brazil. We used pitfall traps baited separately with cow and horse dung, and collected a total of 456 dung beetles, comprising 23 species from 13 different genera. We analysed patterns of alpha and beta diversity, community structure, and species composition among pastures and bait types. Cow dung harboured significantly more species, but a similar abundance of dung beetles compared with horse dung. However, both dung types supported species exclusive to that type, and hosted a distinct dung beetle community structure and composition. Although livestock (cattle and horses) was introduced to Brazil less than 500 years ago, our data suggest that novel and well‐structured dung beetle communities are actively exploiting these novel food resources in Brazilian pasturelands.

DIVERSITY OF SULFATE‐REDUCING GENES (dsrAB) IN SEDIMENTS FROM PUGET SOUND

The aims of this study were to characterize the population structure and diversity of sulfate‐reducing bacteria (SRB) from three distinct sites at Puget Sound, and relate the biogeochemical properties of the sediments to the sulfate‐reducer communities. The population composition and diversity of sulfate‐reducing bacteria carrying dsrAB genes from surface Puget Sound sediments was investigated using a polymerase chain reaction‐based cloning approach. Sediment cores were collected from three different locations: Carr Inlet (C1A), Shallow Bud Inlet (S1A), and Turning Basin (T1A). A total of 498 dsrAB clones were sequenced from the three sites. Ecological indices indicated that T1A had the highest diversity and evenness values and C1A had the lowest. Correlations were also found between diversity indices and geochemical parameters. The diversity of the SRB decreased with decreasing carbon concentrations and sulfate reduction rates, and increasing levels of oxygen. A phylogenetic comparison revealed that the majority of the dsrAB sequences were associated with the delta‐proteobacterial phylotypes Desulfonema, Desulfococcus and Desulfosarcina, suggesting that complete oxidizers with high substrate versatility dominate in the sediments. The environmental conditions and energy sources available in the sediments may have dictated microbial community structure and diversity of SRBs. Distinctive community structures of SRBs in Puget Sound sediments were found to vary at different sites with different redox profiles. The dominance of the Desulfobacteraceae‐like sequences may be due to the presence of a diverse spectrum of substrates in the sediments. This study represents one of the first efforts to characterize the population of sulfate‐reducing microbes in the oxygenated regions of Puget Sound sediments. The phylogenetic identification of dsrAB genes in the sediment samples allows the composition of sulfate‐reducing prokaryotic communities to be inferred, and working hypotheses about their likely carbon substrates to be formed.

Long-term fertilization regimes affect bacterial community structure and diversity of an agricultural soil in northern China

Knowledge about shifts of microbial community structure and diversity following different agricultural management practices could improve our understanding of soil processes and thus help us to develop sound management strategies. A long-term fertilization experiment was established in 1989 at Fengqiu (35°00′N, 114°24′E) in northern China. The soil (sandy loam) is classified as aquic inceptisols and has received continuous fertilization treatments since then. The fertilization treatments included control (CK, no fertilizer), chemical fertilizers nitrogen (N) and potassium (K) (NK), phosphorous (P) and K (PK), NP, NPK, organic manure (OM), and half chemical fertilizers NPK plus half organic manure (1/2NPKOM). The objective of this study was to examine if the microbial community structure and diversity were affected by the long-term fertilization regimes. Soil samples were collected from the long-term experimental plots with seven treatments and four replications in April 2006. Microbial DNAs were extracted from the soil samples and the 16S rRNA genes were PCR amplified. The PCR products were analyzed by DGGE, cloning and sequencing. The bacterial community structures and diversity were assessed using the DGGE profiles and the clone libraries constructed from the excised DGGE bands. The bacterial community structure of the OM and PK treatments were significantly different from those of all other treatments. The bacterial community structures of the four Ncontaining treatments (NK, NP, NPK and 1/2NPKOM), as well as CK, were more similar to each other. The changes in bacterial community structures of the OM and PK treatments showed higher richness and diversity. Phylogenetic analyses indicated that Proteobacteria (30.5%) was the dominant taxonomic group of the soil, followed by Acidobacteria (15.3%), Gemmatimonadetes (12.7%), etc. Irrespective of the two fertilization treatments of OM and PK, the cluster analysis showed that bacterial communities of the remaining five treatments of CK, NK, NP, NPK and 1/2NPKOM seemed to be more similar to each other, which indicated the relatively weak effects of the four N-containing treatments on soil bacterial communities. N fertilizer may be considered as a key factor to counteract the effects of other fertilizers on microbial communities. Our results show that long-term fertilization regimes can affect bacterial community structure and diversity of the agricultural soil. The OM and PK treatments showed a trend towards distinct community structures, higher richness and diversity when compared to the other treatments. Contrasting to the positive effects of OM and PK treatments on the bacterial communities, N fertilizer could be considered as a key factor in the soil to counteract the effects of other fertilizers on soil microbial communities. Because of the extremely high abundance and diversity of microorganisms in soil and the high heterogeneity of the soil, it is necessary to further examine the effects of fertilization regimes on microbial community and diversity in different type soils for comprehensively understanding their effects through the appropriate combination of molecular approaches.

Macroinvertebrate communities of non‐glacial high altitude intermittent streams

Summary1. Macroinvertebrate assemblages of five non‐glacial intermittent high altitude headwater streams (above 1400 m – Serra da Estrela, Portugal), with dry periods of different lengths (0–3 months), were investigated in nearly undisturbed conditions to (i) examine spatial differences and identify environmental variables responsible for the observed invertebrate patterns, (ii) assess the association of dry period length with invertebrate community structure and (iii) determine the influence of using different taxonomic identification levels (order, family and genus) to assess invertebrate community patterns.2. More than 100 macroinvertebrate genera were identified. Insects clearly dominated these communities with more than 95% of total captures and around 95% of the total richness. Diptera were the most rich and abundant group with chironomid occurrences comprising over 70% of macroinvertebrate captures.3. The highest taxon richness, diversity, EPT (Ephemeroptera + Plecoptera + Trichoptera) and OCH (Odonata + Coleoptera + Heteroptera) genus richness, the greatest number of exclusive and characteristic taxa identified by the Indicator Value (IndVal), and a distinct community structure shown by Canonical Correspondence Analyses (CCA), were found in the only stream that was never totally dry, with pools lasting over summer. Environmental gradients that spatially structured the macroinvertebrate communities were always related to flow variations.4. Over time, the highest abundances found in these systems were also related to flow variations and maximum genus richness occurred in the connected pools or in isolated pools. Streams with longer dry periods presented a distinct recolonization phase, with higher abundance of the stonefly larvae Nemoura sp. and the presence of the chironomid larvae Krenosmittia sp., possibly arriving from the hyporheos.5. Taxonomic level of invertebrate identification was vital for recognizing the characteristic taxa (IndVal) of streams yet was not critical for identifying streams with the highest macroinvertebrate richness/diversity or structuring environmental gradients.6. Overall, this study emphasizes the variability of high altitude intermittent streams macroinvertebrate communities, despite spatial proximity. This variability was probably related to flow intermittency and hydrologic permanence, different vegetation covers and riverbed substrata. Consequently, the establishment of reference conditions should involve long‐term data collections and more detailed physical characterization. Also, these findings have significant implications for accurately predicting the ecological consequences of future climate change in high altitude scenarios.

Intra-oral microbial profiles of beagle dogs assessed by checkerboard DNA–DNA hybridization using human probes

Some investigators suggest a similarity between the oral microbiota of dogs and humans. The in vivo assessment of ecologic relationships among bacterial species and between bacterial species and their habitat is difficult to carry out. Consequently, this aspect is often neglected in animal oral microbiological studies. This study aimed to examine the proportions of 40 bacterial species in samples from five intra-oral habitats in beagle dogs using checkerboard DNA–DNA hybridization. Microbial samples were taken from subgingival and supra-gingival plaque, the tongue, tonsils and cheek mucosa in seven beagle dogs. Samples were individually evaluated for their content of 40 bacterial species and the percentage of total DNA probe count was determined for each species, at each habitat. All tested species could be detected in all sampled habitats but each habitat had a distinct community structure. The microbiotas colonizing the hard surfaces in the oral cavity were quite different from the microbiotas colonizing the soft tissues. Bacterial species that are in humans considered to be periodontopathogens are present in high proportions. This study underlines the importance of the habitat and the host on the local microbial profile.

Metal Ions May Suppress or Enhance Cellular Differentiation in Candida albicans and Candida tropicalis Biofilms

Candida albicans and Candida tropicalis are polymorphic fungi that develop antimicrobial-resistant biofilm communities that are characterized by multiple cell morphotypes. This study investigated cell type interconversion and drug and metal resistance as well as community organization in biofilms of these microorganisms that were exposed to metal ions. To study this, Candida biofilms were grown either in microtiter plates containing gradient arrays of metal ions or in the Calgary Biofilm Device for high-throughput susceptibility testing. Biofilm formation and antifungal resistance were evaluated by viable cell counts, tetrazolium salt reduction, light microscopy, and confocal laser scanning microscopy in conjunction with three-dimensional visualization. We discovered that subinhibitory concentrations of certain metal ions (CrO(4)(2-), Co(2+), Cu(2+), Ag(+), Zn(2+), Cd(2+), Hg(2+), Pb(2+), AsO(2)(-), and SeO(3)(2-)) caused changes in biofilm structure by blocking or eliciting the transition between yeast and hyphal cell types. Four distinct biofilm community structure types were discerned from these data, which were designated "domed," "layer cake," "flat," and "mycelial." This study suggests that Candida biofilm populations may respond to metal ions to form cell-cell and solid-surface-attached assemblages with distinct patterns of cellular differentiation.

Afforestation of moorland leads to changes in crenarchaeal community structure

Group 1 Crenarchaeota are an abundant component of soil microbial communities. A number of distinct lineages have been discovered, and the Group 1.1b lineage is present in most soil types. Others, such as the Group 1.1c lineage, may be restricted to specific soil types, such as acidic forest soils. To determine the effects of afforestation on the Archaea of moorland soils, archaeal community structure was examined across three parallel 180 m transects, running from open heather moorland into a Scots pine forest. Communities were characterized using a combination of cloning and denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA reverse transcriptase-polymerase chain reaction products. Although forest soils selected for a reproducibly distinct crenarchaeal community structure from moorland soils, both habitats contained similar populations, indicated by comigrating DGGE bands. Archaeal communities in soils of both ecosystems were dominated by Group 1.1c crenarchaea, and reproducible differences in community structure within this lineage were observed between forest and moorland soils. The findings indicate that the afforestation of moorland soils can lead to changes in crenarchaeal community structure with a potential impact on ecosystem function.

Linking geochemical processes with microbial community analysis: successional dynamics in an arsenic‐rich, acid‐sulphate‐chloride geothermal spring

ABSTRACTThe source waters of acid‐sulphate‐chloride (ASC) geothermal springs located in Norris Geyser Basin, Yellowstone National Park contain several reduced chemical species, including H2, H2S, As(III), and Fe(II), which may serve as electron donors driving chemolithotrophic metabolism. Microorganisms thriving in these environments must also cope with high temperatures, low pH (∼3), and high concentrations of sulphide, As(III), and boron. The goal of the current study was to correlate the temporal and spatial distribution of bacterial and archaeal populations with changes in temperature and geochemical energy gradients occurring throughout a newly formed (redirected) outflow channel of an ASC spring. A suite of complimentary analyses including aqueous geochemistry, microscopy, solid phase identification, and 16S rDNA sequence distribution were used to correlate the appearance of specific microbial populations with biogeochemical processes mediating S, Fe, and As cycling and subsequent biomineralization of As(V)‐rich hydrous ferric oxide (HFO) mats. Rapid As(III) oxidation (maximum first order rate constants ranged from 4 to 5 min−1, t1/2 = 0.17 − 0.14 min) was correlated with the appearance of Hydrogenobaculum and Thiomonas–like populations, whereas the biogenesis of As(V)‐rich HFO microbial mats (mole ratios of As:Fe ∼0.7) was correlated with the appearance of Metallosphaera, Acidimicrobium, and Thiomonas–like populations. Several 16S sequences detected near the source were closely related to sequences of chemolithotrophic hyperthermophilic populations including Stygiolobus and Hydrogenobaculum organisms that are known H2 oxidizers. The use of H2, reduced S(–II,0), Fe(II) and perhaps As(III) by different organisms represented throughout the outflow channel was supported by thermodynamic calculations, confirming highly exergonic redox couples with these electron donors. Results from this work demonstrated that chemical energy gradients play an important role in establishing distinct community structure as a function of distance from geothermal spring discharge.

Microbial Biomass and Community Structure in a Sequence of Soils with Increasing Fertility and Changing Land Use.

The microbial biomass and community structure of eight Chinese red soils with different fertility and land use history was investigated. Two community based microbiological measurements, namely, community level physiological profiling (CLPP) using Biolog sole C source utilization tests and phospholipid fatty acid (PLFA) profiles, were used to investigate the microbial ecology of these soils and to determine how land use alters microbial community structure. Microbial biomass-C and total PLFAs were closely correlated to organic carbon and total nitrogen, indicating that these soil microbial measures are potentially good indices of soil fertility in these highly weathered soils. Metabolic quotients and C source utilization were not correlated with organic carbon or microbial biomass. Multivariate analysis of sole carbon source utilization patterns and PLFAs demonstrated that land use history and plant cover type had a significant impact on microbial community structure. PLFAs showed these differences more than CLPP methods. Consequently, PLFA analysis was a better method for assessing broad-spectrum community differences and at the same time attempting to correlate changes with soil fertility. Soils from tea orchards were particularly distinctive in their CLPP. A modified CLPP method, using absorbance readings at 405 nm and different culture media at pH values of 4.7 and 7.0, showed that the discrimination obtained can be influenced by the culture conditions. This method was used to show that the distinctive microbial community structure in tea orchard soils was not, however, due to differences in pH alone.

Summer dynamics of the coastal planktonic food web in the northern Baltic Sea

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 151:27-41 (1997) - doi:10.3354/meps151027 Summer dynamics of the coastal planktonic food web in the northern Baltic Sea Uitto A, Heiskanen AS, Lignell R, Autio R, Pajuniemi R Summer carbon flow in the pelagic food web was studied within the coastal region of the northern Baltic Sea. Heterotrophic nanoflagellates (HNAN) transferred carbon from picoplankton to ciliates, while ciliates linked nano- and metazooplankton. Hydrodynamic conditions affected the planktonic community, and 3 different periods characterised by distinct community structure and carbon flow dynamics could be distinguished. All trophic groups were largely omnivorous, but the role of herbivory and feeding on heterotrophs varied during summer. In early June, an upwelling mixed the upper water layer. The water column was rich in detritus, remnants from the preceding spring phytoplankton bloom. Phytoplankton was dominated by >10 µm phytoplankton, that was grazed by metazooplankton and heterotrophic dinoflagellates. At the same time HNAN were largely bacteriovorous, thus the microbial food web (MFW) could transfer bacterial carbon to ciliates and metazooplankton. In July during strong thermal stratification the biomass of <10 µm phytoplankton increased, and protists became the most important herbivores. In addition to grazing, metazooplankton gained nanophytoplankton carbon through the MFW by feeding on ciliates. Strong horizontal currents due to upwelling destroyed the stable mid-summer community in late July. Primary production, the biomass of phytoplankton and metazooplankton declined abruptly, whereas the detritus pool increased again. Because all trophic groups fed largely on heterotrophs, the efficiency of the MFW in transferring bacterial carbon to metazooplankton was estimated to be at its highest. When integrated throughout the summer, primary production was 20.5 g m-2, from which sedimentation, herbivory by protists and herbivory by metazooplankton accounted for 27, 40 and 26%, respectively. Bacterial production was 8 g m-2, from which HNAN and ciliates grazed approximately 60%. Excepting the sedimentation in early June, carbon was mostly recycled within the planktonic community during the summer. Primary production · Bacterial production · Sedimentation · Grazing food chain · Microbial food web · Trophic interactions Full text in pdf format PreviousNextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 151. Publication date: May 22, 1997 Print ISSN:0171-8630; Online ISSN:1616-1599 Copyright © 1997 Inter-Research.

Literally spinsters: a new interpretation of local economy and demography in Colyton in the seventeenth and eighteenth centuries

The author investigates reasons for observed changes in the number of marriages and baptisms and in female age at marriage in Colyton England in the seventeenth and eighteenth centuries. She aims to extend the demographic analysis already carried out for the parish of Colyton in Devon and to place it in a social and economic context. The author has linked additional records of the parish such as poor relief documents to the original reconstitution. The most important addition to the present interpretation of Colytons past is the discovery of a low sex ratio. This is associated with domestic industry in the town. It resulted in a distinctive socio-economic community structure. (EXCERPT)

The biomass, community structure, and spatial distribution of the sedimentary microbiota from a high-energy area of the deep sea

Sediments from an abyssal area subjected to high-energy currents showed a total cellular biomass, measured as extractable phospholipid, 6 to 10 times greater than that of other sediments of comparable depths, and approximately one-third that of a subtidal estuarine sediment. Community structure of these abyssal sediments, assessed by ester-linked phospholipid fatty acids, was characterized by increased bacterial dominance and a greater proportion of anaerobic bacteria when compared to a subtidal estuarine sediment. Although there is geochemical evidence for mixing of sediments to depths > 10 cm below the sediment surface, biomass in the 9 to 10 cm layer is approximately one-third of the 0 to 1 cm layer. A distinct community structure occurs in this deeper stratum, as reflected by increased proportions of fatty acids typical of anaerobic bacteria. A three-level, nested sampling design allowed an assessment of spatial distribution of microbial assemblies. The major source of variance was among subcores within a box core. This small-scale patchiness parallels that determined for a subtidal estuarine sediment.

Weather and climate of the antarctic

Permafrost degradation due to climate warming would potentially increase the release of previously frozen soil carbon and change the carbon budget of the cold region ecosystem. The underlying permafrost degradation would be effectively mediated by soil surface freezing-thawing (FT) processes. Aboveground vegetation can regulate soil FT processes, however its effects on ground thermal transfer have not been well represented by ecosystem models. In this study, we improved the hydrothermal module of the Boreal Ecosystem Productivity Simulator (BEPS) through more careful parameterization of snowpack density, puddled water, soil organic matter and super-cooled soil water. The impacts of vegetation on the soil surface FT processes have also been investigated using the improved BEPS model and the measured soil temperature data at forest and grassland sites on the southern edge of permafrost region in Mongolia and northeastern China. The improved BEPS model performs better than the original model in simulations of soil temperature and soil FT processes. Smaller amplitudes of soil diurnal FT cycles were found in forest sites compared to grassland sites. Forest sites have delayed soil thaw timing and similar soil freezing time compared to grassland sites. Differences in snow depths and soil organic matter content due to distinct vegetation community structures have considerable influences on the disparity in soil FT processes. Thus, it is important to improve the simulation of the impacts of vegetation on soil surface FT processes for better forecasting the permafrost degradation.

Fungi Associated with the Decomposition of the Black Rush,Juncus Roemerianus, in South Florida

To determine what fungi are associated with the decomposition process and what affects certain environmental and sampling variables have on the observed fungal community structure, the fungi associated with Juncus roemerianus in a subtropical environment were examined. A total of 123 fungal taxa was observed on Juncus roemerianus leaves. Thirty-four taxa were at a frequency of occurrence of 1% or more. Of these, 5 taxa (Fusarium spp., Cladosporium cladosporioides, Drechslera hawaiiensis, Alternaria alternata and Geniculosporium sp.) were in excess of 25%. The observed community structure was affected by the condition of the leaf (living, senescent or decomposing leaves), position on the leaf (tip, middle or base of the leaf), season of the year (wet vs dry season) and culture technique. Of less significance was station location within the study site. Comparisons with other studies of Juncus and red mangrove (Rhizophora mangle) litter indicated a distinct fungal community structure associated with Juncus in subtropical estuarine environments. 29 references, 10 tables. (ACR)