Changes In Microbial Community Composition Research Articles

Interactive effects of precipitation and nitrogen spatial pattern on carbon use and functional diversity in soil microbial communities

Impacts of climate change drivers on soil biota and biogeochemical cycling are of growing concern. Soil nitrogen (N) availability has the potential to mediate microbial responses to changes in precipitation via changes in microbial community composition, but the interactions between N spatial pattern and rainfall regime on soil microbial community structure and function remain unclear. We conducted an outdoor mesocosm experiment with a model grassland community to assess interactive effects of rainfall amount (control, −50% rainfall, +50% rainfall) and N spatial pattern (homogeneous, heterogeneous) on bacterial carbon (C) use and functional diversity using a community-level physiological profiling approach. Patchy N addition increased total bacterial C use and diversity of substrate use irrespective of rainfall treatment. Observed increases in microbial functional diversity contrasted with patch-induced decreases in plant community diversity in the study system. Neither bacterial C use nor diversity of C sources showed a significant response to rainfall regime or a significant rainfall×N pattern interaction. However, Principal Components Analysis showed clustering of bacterial substrate use across treatments, in line with different strategies of C use linked to both N spatial pattern and rainfall regime. Our findings suggest that bacterial substrate profiles are more sensitive to dry conditions when soil N is patchily distributed, with significant implications for soil organic C composition and storage potential in heterogeneous grasslands under future climatic conditions.

Sequential Changes of Microbial Community Composition During Biological Wastewater Treatment in Single Unit Waste Stabilization System

Kolkata city sewage purification process is rapid, extremely efficient and the process is operated in single pond systems at East Kolkata Wetland (EKW) in a highly sustainable manner. However, the underlying mechanism remains unclear. Since microbial activity plays vital role in wastewater purification, an understanding of the microbial community structure and their functions during purification is crucial. Therefore, we investigated the microbial community structure at different phases of this purification process. To unveil the microbial community structure, we performed 16S rDNA-based community analysis. The microbial community was found to be composed of methane producing, sulphate reducing, ammonia oxidising, nitrifying, denitrifying, phosphorus accumulating and other types of microorganisms. Results also showed that microbes with versatile metabolic potential grow at different phases of purification process and the microbial diversity and complexity decreases considerably with the progression of purification. Beside this, studies on the distribution of microbial population reveals that the community achieves more stability at later phases of purification. Thus, the current study documents the variations in microbial community structure during wastewater purification in single pond unit at EKW and provides an insight into the underlying mechanism of this type of unique process.

Selective Spectrum Antibiotic Modulation of the Gut Microbiome in Obesity and Diabetes Rodent Models.

The gastrointestinal tract microbiome has been suggested as a potential therapeutic target for metabolic diseases such as obesity and Type 2 diabetes mellitus (T2DM). However, the relationship between changes in microbial communities and metabolic disease-phenotypes are still poorly understood. In this study, we used antibiotics with markedly different antibacterial spectra to modulate the gut microbiome in a diet-induced obesity mouse model and then measured relevant biochemical, hormonal and phenotypic biomarkers of obesity and T2DM. Mice fed a high-fat diet were treated with either ceftazidime (a primarily anti-Gram negative bacteria antibiotic) or vancomycin (mainly anti-Gram positive bacteria activity) in an escalating three-dose regimen. We also dosed animals with a well-known prebiotic weight-loss supplement, 10% oligofructose saccharide (10% OFS). Vancomycin treated mice showed little weight change and no improvement in glycemic control while ceftazidime and 10% OFS treatments induced significant weight loss. However, only ceftazidime showed significant, dose dependent improvement in key metabolic variables including glucose, insulin, protein tyrosine tyrosine (PYY) and glucagon-like peptide-1 (GLP-1). Subsequently, we confirmed the positive hyperglycemic control effects of ceftazidime in the Zucker diabetic fatty (ZDF) rat model. Metagenomic DNA sequencing of bacterial 16S rRNA gene regions V1-V3 showed that the microbiomes of ceftazidime dosed mice and rats were enriched for the phylum Firmicutes while 10% OFS treated mice had a greater abundance of Bacteroidetes. We show that specific changes in microbial community composition are associated with obesity and glycemic control phenotypes. More broadly, our study suggests that in vivo modulation of the microbiome warrants further investigation as a potential therapeutic strategy for metabolic diseases.

Multiple‐stressor effects on leaf litter decomposition and fungal decomposers in agricultural streams contrast between litter species

Summary Agricultural land use commonly exerts multiple stressors on the functioning of stream ecosystems, including leaf litter decomposition and the utilization of this resource in stream food webs. If stressors interact, their cumulative effects on biotic responses cannot be predicted from knowledge of individual stressor effects, posing challenges for management and restoration of ecosystems. We examined the individual and interactive effects of four common agricultural stressors and the role of litter quality on leaf litter decomposition and fungal decomposers. In 128 outdoor, flow‐through mesocosms, we manipulated levels of nutrients, a nitrification inhibitor (dicyandiamide), deposited fine sediment and flow velocity. Interactions among these stressors can ensue because, for instance, they jointly affect physicochemical conditions around leaf litter colonized by fungi such as concentrations of dissolved oxygen and nutrients. The two litter species used, deciduous birch and evergreen mahoe, showed contrasting decomposition dynamics, and these differences influenced their response to stressors. Fungi were important for birch litter decomposition but played a minor role for mahoe. Overall, flow velocity reduction and deposited fine sediment had the strongest, mainly negative effects on fungi and litter decomposition, probably as a consequence of reductions in dissolved oxygen available to fungi. However, fine sediment substantially increased mahoe litter mass loss, pointing at fungi‐independent processes being relevant for its decomposition. Although interactions among stressors were uncommon, they showed effects of the same magnitude as stressor main effects. Potential mechanisms underlying interactions included reductions in dissolved oxygen and changes in microbial community composition. Knowledge of the effects of multiple agricultural stressors and of litter quality on litter decomposition and litter‐associated fungi is crucial for management of forested riparian corridors, which have been shown to efficiently mitigate impacts of agricultural stressors on streams. The contrasting responses of the litter species used in our study warrant consideration of species composition of the riparian vegetation.

Molecular Assessment of Bacterial Community Dynamics and Functional End Points during Sediment Bioaccumulation Tests.

Whole sediment toxicity tests play an important role in environmental risk assessment of organic chemicals. It is not clear, however, to what extent changing microbial community composition and associated functions affect sediment test results. We assessed the development of bacterial communities in artificial sediment during a 28 day bioaccumulation test with polychlorinated biphenyls, chlorpyrifos, and four marine benthic invertebrates. DGGE and 454-pyrosequencing of PCR-amplified 16S rRNA genes were used to characterize bacterial community composition. Abundance of total bacteria and selected genes encoding enzymes involved in important microbially mediated ecosystem functions were measured by qPCR. Community composition and diversity responded most to the time course of the experiment, whereas organic matter (OM) content showed a low but significant effect on community composition, biodiversity and two functional genes tested. Moreover, OM content had a higher influence on bacterial community composition than invertebrate species. Medium OM content led to the highest gene abundance and is preferred for standard testing. Our results also indicated that a pre-equilibration period is essential for growth and stabilization of the bacterial community. The observed changes in microbial community composition and functional gene abundance may imply actual changes in such functions during tests, with consequences for exposure and toxicity assessment.

Nutrient-cycling microbes in coastal Douglas-fir forests: regional-scale correlation between communities, in situ climate, and other factors.

Microbes such as fungi and bacteria play fundamental roles in litter-decay and nutrient-cycling; however, their communities may respond differently than plants to climate change. The structure (diversity, richness, and evenness) and composition of microbial communities in climate transects of mature Douglas-fir stands of coastal British Columbia rainshadow forests was analyzed, in order to assess in situ variability due to different temperature and moisture regimes. We compared denaturing gradient gel electrophoresis profiles of fungi (18S-FF390/FR1), nitrogen-fixing bacteria (NifH-universal) and ammonia-oxidizing bacteria (AmoA) polymerase chain reaction amplicons in forest floor and mineral soil samples from three transects located at different latitudes, each transect spanning the Coastal Western Hemlock and Douglas-fir biogeoclimatic zones. Composition of microbial communities in both soil layers was related to degree days above 0°C (2725–3489), while pH (3.8–5.5) best explained shifts in community structure. At this spatial scale, climatic conditions were likely to directly or indirectly select for different microbial species while local site heterogeneity influenced community structure. Significant changes in microbial community composition and structure were related to differences as small as 2.47% and 2.55°C in mean annual moisture and temperature variables, respectively. The climatic variables best describing microbial composition changed from one functional group to the next; in general they did not alter community structure. Spatial distance, especially associated with latitude, was also important in accounting for community variability (4–23%); but to a lesser extent than the combined influence of climate and soil characteristics (14–25%). Results suggest that in situ climate can independently account for some patterns of microbial biogeography in coastal Douglas-fir forests. The distribution of up to 43% of nutrient-cycling microorganisms detected in forest soils responded to smaller abiotic gradients than host trees.

Fertilization practices alter microbial nutrient limitations after alleviation of carbon limitation in a Ferric Acrisol

Microbial nutrient limitation was investigated in a 53-year-old field experiment in the Central-West of Burkina Faso under sorghum–cowpea rotation, comparing three fertilization practices: mineral fertilizer (MIN), mineral fertilizer and farmyard manure (MINFYM), and a non-fertilized control (CON). We assessed microbial N and P limitation after removal of C limitation by (i) determining microbial N and P, (ii) assessing respiration kinetics in incubated soil samples amended with easily available C (glucose) alone or in combination with N and/or P, or not amended, and (iii) evaluating changes in microbial biomass and community composition at the peak of microbial respiration by microbial P and phospholipid fatty acid (PLFA) analyses. Microbial N and P were very low in all fertilization practices, but greater in MINFYM than in CON. Easily available C was the first factor limiting microorganisms in all fertilization practices. After removal of C limitation, most indicators suggested N and P co-limitation in CON. In contrast, respiration kinetics in MINFYM and MIN were only N-limited, while biomass formation in MINFYM was also P-limited. PLFA analyses indicated preferential fungal growth on the added C, and P limitation of changes in microbial community composition in MIN. Long-term application of fertilizers mostly alleviated secondary microbial nutrient limitation by P but not by N, and C always remained the primary limiting factor for microbial growth.

Temporal dynamics and variation with forest type of phospholipid fatty acids in litter and soil of temperate forests across regions

Microorganisms form the basis of soil food webs and represent key control points of carbon cycling and sequestration. Virtually all central European forests are managed and land-use regimes likely impact microbial abundance and community composition. Consequently, knowledge on how land-use intensity and abiotic variables, such as pH, C-to-N ratios, moisture regimes and concomitantly different stress levels, affect microbial communities is needed. We investigated phospholipid fatty acid (PLFA) profiles of leaf litter and soil from four forest types differing in foliage, age and management intensity, replicated in three regions across Germany. To account for temporal variation, samples were taken twice in the same season, but with an interval of three years. Total microbial biomass and microbial community composition differed between years, presumably due to between year variations in weather conditions. The litter layer was more prone to effects of drying, with a reduction of almost 30% of total PLFAs in the drier year. In soil effects of weather conditions depended on soil type and therefore differed between regions, with microorganisms in the sandy soils of the Schorfheide being more susceptible to water-stress, as evidenced by a ten-fold increase of the stress indicator cy/pre ratio in the drier year. Despite temporal variations in microbial biomass and community composition, the balance between the fungal and bacterial energy channel, as measured by fungal-to-bacterial ratios, remained rather constant in particular in soil. While total microbial biomass did not differ between forest types, microbial community composition differed significantly between beech and coniferous forests. Despite more acidic conditions, the fungal energy channel was less pronounced in leaf litter of coniferous forests than in broad-leaved forests, whereas the proportion of bacterial fatty acids was the highest in coniferous forests. Increasing management intensity presumably fosters the bacterial energy channel in the exposed litter layer. Supporting this assumption coniferous forests featured significantly higher values of the stress indicators cy/pre and SAT/MONO ratio. Bacterial community structure and biomass closely correlated with pH, with particular PLFAs dominating at high and low pH, respectively, indicating pH-specific microbial communities. In contrast, fungal abundance in leaf litter was correlated with C-to-N ratio. The results suggest that leaf litter and soil need to be considered separately when investigating changes in microbial community composition, since susceptibility of microorganisms to environmental stressors differs markedly between these layers. This, and repeated sampling events, may be particularly important when investigating subtle effects such as those related to climate change.

Herbicide Persistence in Seawater Simulation Experiments.

Herbicides are detected year-round in marine waters, including those of the World Heritage listed Great Barrier Reef (GBR). The few previous studies that have investigated herbicide persistence in seawater generally reported half-lives in the order of months, and several studies were too short to detect significant degradation. Here we investigated the persistence of eight herbicides commonly detected in the GBR or its catchments in standard OECD simulation flask experiments, but with the aim to mimic natural conditions similar to those found on the GBR (i.e., relatively low herbicide concentrations, typical temperatures, light and microbial communities). Very little degradation was recorded over the standard 60 d period (Experiment 1) so a second experiment was extended to 365 d. Half-lives of PSII herbicides ametryn, atrazine, diuron, hexazinone and tebuthiuron were consistently greater than a year, indicating high persistence. The detection of atrazine and diuron metabolites and longer persistence in mercuric chloride-treated seawater confirmed that biodegradation contributed to the breakdown of herbicides. The shortest half-life recorded was 88 d for growth-regulating herbicide 2,4-D at 31°C in the dark, while the fatty acid-inhibitor metolachlor exhibited a minimum half-life of 281 d. The presence of moderate light and elevated temperatures affected the persistence of most of the herbicides; however, the scale and direction of the differences were not predictable and were likely due to changes in microbial community composition. The persistence estimates here represent some of the first appropriate data for application in risk assessments for herbicide exposure in tropical marine systems. The long persistence of herbicides identified in the present study helps explain detection of herbicides in nearshore waters of the GBR year round. Little degradation of these herbicides would be expected during the wet season with runoff and associated flood plumes transporting a high proportion of the original herbicide from rivers into the GBR lagoon.

Linking Jasmonic Acid Signaling, Root Exudates, and Rhizosphere Microbiomes.

Jasmonic acid (JA) is an essential hormone in plant development and defense responses in Arabidopsis thaliana. Exogenous treatment with JA has recently been shown to alter root exudate profiles and the composition of root-associated bacterial communities. However, it is currently unknown whether disruptions of the JA in the rhizosphere affect root exudation profiles and the relative abundance of bacteria and archaea in the rhizosphere. In the present study, two Arabidopsis mutants that are disrupted in different branches of the jasmonate pathway, namely myc2 and med25, were cultivated in nutrient solution and soil to profile root exudates and bacterial and archaeal communities, respectively. Compared with the wild type, both mutants showed distinct exudation patterns, including lower amounts of asparagine, ornithine, and tryptophan, as well as distinct bacterial and archaeal community composition, as illustrated by an increased abundance of Streptomyces, Bacillus, and Lysinibacillus taxa in the med25 rhizosphere and an Enterobacteriaceae population in myc2. Alternatively, the Clostridiales population was less abundant in the rhizosphere of both mutants. Similarities between plant genotypes were highly correlated, as determined by operational taxonomic units in the rhizosphere and metabolites in root exudates. This strongly suggests that root exudates play a major role in modulating changes in microbial community composition upon plant defense responses.

Uncultured Desulfobacteraceae and Crenarchaeotal group C3 incorporate 13C-acetate in coastal marine sediment.

Stable isotope probing (SIP) of deoxyribonucleic acid (DNA) was used to identify microbes incorporating (13) C-labeled acetate in sulfate-reducing sediment from Aarhus Bay, Denmark. Sediment was incubated in medium containing 10 mM sulfate and different (13) C-acetate (10, 1, 0.1 mM) concentrations. The resultant changes in microbial community composition were monitored in total and SIP-fractionated DNA during long-term incubations. Chemical analyses demonstrated metabolic activity in all sediment slurries, with sulfate-reducing activity largely determined by initial acetate concentrations. Sequencing of 16S rRNA gene PCR amplicons showed that the incubations shifted the bacterial but not the archaeal community composition. After 3 months of incubation, only sediment slurries incubated with 10 mM (13) C-acetate showed detectable (13) C-DNA labeling. Based on 16S rRNA and dsrB gene PCR amplicon sequencing, the (13) C-labeled DNA pool was dominated by a single type of sulfate reducer representing a novel genus in the family Desulfobacteraceae. In addition, members of the uncultivated Crenarchaeotal group C3 were enriched in the (13) C-labeled DNA. Our results were reproducible across biological replicate experiments and provide new information about the identities of uncultured acetate-consuming bacteria and archaea in marine sediments.

Impact of tropical lowland rainforest conversion into rubber and oil palm plantations on soil microbial communities

Focusing on Sumatra, a hotspot of tropical lowland rainforest transformation, we investigated effects of the con- version of rainforests into rubber agroforests (Bjungle rubber^), intensive rubber, and oil palm plantations on the communities of litter and soil microorganisms and identified factors responsible for these changes. Litter basal respiration, microbial biomass, total bacterial phospholipid fatty acids (PLFAs), and fungal PLFAs did not vary significantly with rainforest conversion. In litter of converted ecosystems, the concentration of certain PLFAs including the Gram-negative bacteria marker PLFA cy17:0 and the Gram-positive bacteria marker PLFA i17:0 was reduced as compared to rainforest, whereas the concentration of the arbuscular mycorrhizal fungi (AMF) marker neutral lipid fatty acid (NLFA) 16:1ω5c in- creased. As indicated by redundancy analysis, litter pH and carbon concentration explained most of the variation in litter microbial community composition. In soil, microbial biomass did not vary significantly with rainforest conversion, whereas basal respiration declined. Total PLFAs and especially that of Gram-negative bacteria decreased, whereas PLFA i17:0 in- creased with rainforest conversion. The concentration of fun- gal PLFAs increased with rainforest conversion, whereas NLFA 16:1ω5c did not change significantly. Redundancy analysis indicated that soil pH explained most of the variation in soil microbial community composition. Overall, the data suggest that conversion of rainforests into production systems results in more pronounced changes in microbial community composition in soil as compared to litter. In particular, the response of fungi and bacteria was more pronounced in soil, while the response of AMF was more pronounced in litter. Notably, only certain bacterial markers but not those of saprotrophic fungi and AMF were detrimentally affected by rainforest conversion.

Effects of diurnal temperature variation on microbial community and petroleum hydrocarbon biodegradation in contaminated soils from a sub-Arctic site.

Contaminated soils are subject to diurnal and seasonal temperature variations during on-site ex-situ bioremediation processes. We assessed how diurnal temperature variations similar to that in summer at the site from which petroleum hydrocarbon-contaminated soil was collected affect the soil microbial community and the extent of biodegradation of petroleum hydrocarbons compared with constant temperature regimes. Microbial community analyses for 16S rRNA and alkB genes by pyrosequencing indicated that the microbial community for soils incubated under diurnal temperature variation from 5°C to 15°C (VART5-15) evolved similarly to that for soils incubated at constant temperature of 15°C (CST15). In contrast, under a constant temperature of 5°C (CST5), the community evolved significantly different. The extent of biodegradation of C10-C16 hydrocarbons in the VART5-15 systems was 48%, comparable with the 41% biodegradation in CST15 systems, but significantly higher than CST5 systems at 11%. The enrichment of Gammaproteobacteria was observed in the alkB gene-harbouring communities in VART5-15 and CST15 but not in CST5 systems. However, the Actinobacteria was abundant at all temperature regimes. The results suggest that changes in microbial community composition as a result of diurnal temperature variations can significantly influence petroleum hydrocarbon bioremediation performance in cold regions.

Effects of Different Organic Manures on the Biochemical and Microbial Characteristics of Albic Paddy Soil in a Short-Term Experiment

This study aimed to evaluate the effects of chemical fertilizer (NPK), NPK with livestock manure (NPK+M), NPK with straw (NPK+S), and NPK with green manure (NPK+G) on soil enzyme activities and microbial characteristics of albic paddy soil, which is a typical soil with low productivity in China. The responses of extracellular enzyme activities and the microbial community diversity (determined by phospholipid fatty acid analysis [PLFA] and denaturing gradient gel electrophoresis [DGGE]) were measured. The results showed that NPK+M and NPK+S significantly increased rice yield, with NPK+M being approximately 24% greater than NPK. The NPK+M significantly increased soil organic carbon (SOC) and available phosphate (P) and enhanced phosphatase, β-cellobiosidase, L-leucine aminopeptidase and urease activities. The NPK+S significantly increased SOC and available potassium (K) and significantly enhanced N-acetyl-glucosamidase, β-xylosidase, urease, and phenol oxidase activities. The NPK+G significantly improved total nitrogen (N), ammonium N, available P, and N-acetyl-glucosamidase activity. The PLFA biomass was highest under NPK+S, followed by NPK+M and NPK+G treatments. Principal component analysis (PCA) of the PLFA indicated that soils with NPK+M and NPK+S contained higher proportions of unsaturated and cyclopropane fatty acids (biomarkers of fungi and gram-negative bacteria) and soil under NPK+G contained more straight chain saturated fatty acids (representing gram-positive bacteria). PCA of the DGGE patterns showed that organic amendments had a greater influence on fungal community. Cluster analysis of fungal DGGE patterns revealed that NPK+G was clearly separated. Meanwhile, the bacterial community of NPK+M treatment was the most distinct. RDA analysis revealed changes of microbial community composition mostly depended on β-xylosidase, β-cellobiosidase activities, total N and available K contents. The abundances of gram-negative bacterial and fungal PLFAs probably effective in improving fertility of low-yield albic paddy soil because of their significant influence on DGGE profile.

Growth of modern branched columnar stromatolites in Lake Joyce, Antarctica

Modern decimeter-scale columnar stromatolites from Lake Joyce, Antarctica, show a change in branching pattern during a period of lake level rise. Branching patterns correspond to a change in cyanobacterial community composition as preserved in authigenic calcite crystals. The transition in stromatolite morphology is preserved by mineralized layers that contain microfossils and cylindrical molds of cyanobacterial filaments. The molds are composed of two populations with different diameters. Large diameter molds (>2.8 μm) are abundant in calcite forming the oldest stromatolite layers, but are absent from younger layers. In contrast, <2.3 μm diameter molds are common in all stromatolites layers. Loss of large diameter molds corresponds to the transition from smooth-sided stromatolitic columns to branched and irregular columns. Mold diameters are similar to trichome diameters of the four most abundant living cyanobacteria morphotypes in Lake Joyce: Phormidium autumnale morphotypes have trichome diameters >3.5 μm, whereas Leptolyngbya antarctica, L. fragilis, and Pseudanabaena frigida morphotypes have diameters <2.3 μm. P. autumnale morphotypes were only common in mats at <12 m depth. Mats containing abundant P. autumnale morphotypes were smooth, whereas mats with few P. autumnale morphotypes contained small peaks and protruding bundles of filaments, suggesting that the absence of P. autumnale morphotypes allowed small-scale topography to develop on mats. Comparisons of living filaments and mold diameters suggest that P. autumnale morphotypes were present early in stromatolite growth, but disappeared from the community through time. We hypothesize that the mat-smoothing behavior of P. autumnale morphotypes inhibited nucleation of stromatolite branches. When P. autumnale morphotypes were excluded from the community, potentially reflecting a rise in lake level, short-wavelength roughness provided nuclei for stromatolite branches. This growth history provides a conceptual model for initiation of branched stromatolite growth resulting from a change in microbial community composition.

Temperature and solids retention time control microbial population dynamics and volatile fatty acid production in replicated anaerobic digesters.

Anaerobic digestion is a widely used technology for waste stabilization and generation of biogas, and has recently emerged as a potentially important process for the production of high value volatile fatty acids (VFAs) and alcohols. Here, three reactors were seeded with inoculum from a stably performing methanogenic digester, and selective operating conditions (37°C and 55°C; 12 day and 4 day solids retention time) were applied to restrict methanogenesis while maintaining hydrolysis and fermentation. Replicated experiments performed at each set of operating conditions led to reproducible VFA production profiles which could be correlated with specific changes in microbial community composition. The mesophilic reactor at short solids retention time showed accumulation of propionate and acetate (42 ± 2% and 15 ± 6% of CODhydrolyzed, respectively), and dominance of Fibrobacter and Bacteroidales. Acetate accumulation (>50% of CODhydrolyzed) was also observed in the thermophilic reactors, which were dominated by Clostridium. Under all tested conditions, there was a shift from acetoclastic to hydrogenotrophic methanogenesis, and a reduction in methane production by >50% of CODhydrolyzed. Our results demonstrate that shortening the SRT and increasing the temperature are effective strategies for driving microbial communities towards controlled production of high levels of specific volatile fatty acids.

Main factors controlling microbial community structure and function after reclamation of a tailing pond with aided phytostabilization

Reclamation on bare tailing ponds has the potential to represent soil genesis in Technosols favoring the understanding of the changes of microbial communities and function. In this study we used phytostabilization aided with calcium carbonate and pig slurry/manure to reclaim an acidic bare tailing pond with the aim of investigating the effect of amending and different species on microbial community structure and function. We sampled after two years of amending and planting: unamended tailing soil (UTS), non-rhizospheric amended tailing soil (ATS), rhizospheric soil from four species, and non-rhizospheric native forest soil (NS), which acted as reference. The application of amendments increased pH up to neutrality, organic carbon (Corg), C/N and aggregate stability, while decreased salinity and heavy metals availability. No effect of rhizosphere was observed on physicochemical properties, metals immobilization and microbial community structure and function. To account for confounding effects due to soil organic matter, microbial properties were expressed per Corg. The high increments in pH and Corg have been the main factors driving changes in microbial community structure and function. Bacterial biomass was higher in UTS, without significant differences among the rest of soils. Fungal biomass followed the trend UTS<ATS=rhizospheric soils<NS. Bacterial growth increased and fungal growth decreased with increasing pH, despite the high availability of metals at low pH. Enzyme activities were lower in UTS, with β-glucosidase and β-glucosaminidase activities highly correlated with bacterial growth. Microbial activities were not correlated with the exchangeable fraction of heavy metals, indicating that microbial function is not strongly affected by these metals, likely due to the efficiency of the reclamation procedure to reduce metals toxicity. Changes in microbial community composition were largely explained by changes in pH, heavy metals availability and Corg, with increments in fungal and actinobacterial proportions with soil amending.

Colonization in the photic zone and subsequent changes during sinking determine bacterial community composition in marine snow.

Due to sampling difficulties, little is known about microbial communities associated with sinking marine snow in the twilight zone. A drifting sediment trap was equipped with a viscous cryogel and deployed to collect intact marine snow from depths of 100 and 400 m off Cape Blanc (Mauritania). Marine snow aggregates were fixed and washed in situ to prevent changes in microbial community composition and to enable subsequent analysis using catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). The attached microbial communities collected at 100 m were similar to the free-living community at the depth of the fluorescence maximum (20 m) but different from those at other depths (150, 400, 550, and 700 m). Therefore, the attached microbial community seemed to be “inherited” from that at the fluorescence maximum. The attached microbial community structure at 400 m differed from that of the attached community at 100 m and from that of any free-living community at the tested depths, except that collected near the sediment at 700 m. The differences between the particle-associated communities at 400 m and 100 m appeared to be due to internal changes in the attached microbial community rather than de novo colonization, detachment, or grazing during the sinking of marine snow. The new sampling method presented here will facilitate future investigations into the mechanisms that shape the bacterial community within sinking marine snow, leading to better understanding of the mechanisms which regulate biogeochemical cycling of settling organic matter.

Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi river water

Microbial decay processes are one of the mechanisms whereby sewage contamination is reduced in the environment. This decomposition process involves a highly complex array of bacterial and eukaryotic communities from both sewage and ambient waters. However, relatively little is known about how these communities change due to mixing and subsequent decomposition of the sewage contaminant. We investigated decay of sewage in upper Mississippi River using Illumina sequencing of 16S and 18S rRNA gene hypervariable regions and qPCR for human-associated and general fecal Bacteroidales indicators. Mixtures of primary treated sewage and river water were placed in dialysis bags and incubated in situ under ambient conditions for seven days. We assessed changes in microbial community composition under two treatments in a replicated factorial design: sunlight exposure versus shaded and presence versus absence of native river microbiota. Initial diversity was higher in sewage compared to river water for 16S sequences, but the reverse was observed for 18S sequences. Both treatments significantly shifted community composition for eukaryotes and bacteria (P < 0.05). Data indicated that the presence of native river microbiota, rather than exposure to sunlight, accounted for the majority of variation between treatments for both 16S (R = 0.50; P > 0.001) and 18S (R = 0.91; P = 0.001) communities. A comparison of 16S sequence data and fecal indicator qPCR measurements indicated that the latter was a good predictor of overall bacterial community change over time (rho: 0.804–0.814, P = 0.001). These findings suggest that biotic interactions, such as predation by bacterivorous protozoa, can be critical factors in the decomposition of sewage in freshwater habitats and support the use of Bacteroidales genetic markers as indicators of fecal pollution.

Temporal changes in microbial community composition during culture enrichment experiments with Indonesian coals

Temporal changes in microbial community structures during methanogenesis were investigated in cultures of South Sumatra Basin (SSB) coalbed methane (CBM) formation water (SSB5) grown on three coals of different rank (Burung sub bituminous Rv 0.39%, Mangus sub bituminous Rv 0.5%, Mangus anthracite Rv 2.2%). Methane production accelerated from day 6, peaked around day 17 and then levelled off around day 20. The initial bacterial community from the SSB formation water was predominantly Acetobacterium, Acidaminobacter, Bacteroides and Pelobacter species, while the archaeal community consisted of Methanosaeta, Methanosarcina and Methanobacterium members. A general pattern was observed in all cultures with the three coals. Over time the bacterial members decreased in proportion whereas the archaeal component increased. The increase in the proportion of archaeal methanogens corresponded with an increase in methane production yield.Enrichment cultures produced similar communities when grown on coals from the same seam (Mangus sub bituminous and Mangus anthracite), rather than from different seams of similar type (Burung sub bituminous and Mangus sub bituminous). Methanosaeta was the dominant methanogen species in the sub bituminous Burung coal culture, but was a lesser proportion in cultures of both Mangus sub bituminous and anthracite coals where Methanosarcina species were a greater proportion. Interestingly, obligate hydrogenotrophic methanogens from the genera of Methanobacterium, which were present at low levels in culture enrichment of all coal substrates, increased in proportion only in the absence of coal in the no-coal control enrichment cultures. These results suggest that the low rank Burung sub bituminous coal favours methane production by the obligate acetoclastic Methanosaeta members while both Mangus coals also favour metabolically versatile Methanosarcina members, and the absence of coal favours hydrogenotrophic methanogens. Despite the similarity of communities grown on coals from the same seam, greater quantities of methane were generated from the lower rank coals when compared to higher rank coals.