Variation In Bacterial Community Composition Research Articles

Comparing Sediment Bacterial Communities of Volcanic Lakes and Surrounding Rivers in Inner Mongolia Autonomous Region, Northeastern China

Volcanic lakes originate from a volcanic crater or caldera, and were a crucial component of aquatic ecosystems. Sediment bacteria play an important role in the nutrient cycling of aquatic ecosystems; however, their patterns distribution in volcanic lakes and the surrounding river habitats are unknown. In this study, we compare the sediment bacterial communities and their co-occurrence networks between these two habitats in the Inner Mongolia Autonomous Region, Northeastern China (the Arxan UNESCO Global Geopark), using 16S rRNA gene amplicon sequencing. The results revealed that there were significant variations in the physicochemical parameters of the sediment between these two habitats. The bacterial α-diversity, β-diversity, and community composition of the sediment also significantly differed between these two habitats. Network analysis showed that the co-occurrence patterns and keystone taxa in the sediment differed between these two habitats. The sediment bacterial communities in the river habitats were more stable than those in the lake habitats in the face of environmental change. Canonical correspondence analysis demonstrated that both physical (pH and MC) and nutrition-related factors (TN, TP, LOI, and TOC) were the most important environmental factors shaping the variations of bacterial community composition (BCC) in the sediment between these two habitats. This work could greatly improve our understanding of the sediment BCC of the sediment from aquatic ecosystems in the UNESCO Global Geopark.

Different effects of seasonal impoundment and land use change on microbiome in a tributary sediment of the three gorgers reservoir

Anthropogenic activities significantly impact river ecosystem nutrient fluxes and microbial metabolism. Here, we examined the seasonal and spatial variation of sediments physicochemical parameters and the associated microbiome in the Pengxi river, a representative tributary of Three Gorges Reservoir, in response to seasonal impoundment and land use change by human activities. Results revealed that seasonal impoundment and land use change enhanced total organic carbon (TOC), total nitrogen (TN) and ammonium nitrogen (NH4+-N) concentration in the sediment, but have different effects on sediment microbiome. Sediment microbiota showed higher similarity during the seasonal high-water level (HWL) in consecutive two years. The abundant phyla Acidobacteria, Gemmatimonadetes, Cyanobacteria, Actinobacteria and Planctomycetes significantly increased as water level increased. Along the changes in bacterial taxa, we also observed changes in predicted carbon fixation functions and nitrogen-related functions, including the significantly higher levels of Calvin cycle, 4HB/3HP cycle, 3HP cycle and assimilatory nitrate reduction, while significantly lower level of denitrification. Though land use change significantly increased TOC, TN and NH4+-N concentration, its effects on spatial variation of bacterial community composition and predicted functions was not significant. The finding indicates that TGR hydrologic changes and land use change have different influences on the carbon and nitrogen fluxes and their associated microbiome in TGR sediments. A focus of future research will be on assessing on carbon and nitrogen flux balance and the associated carbon and nitrogen microbial cycling in TGR sediment.

Afforestation Enhances Potential Bacterial Metabolic Function without Concurrent Soil Carbon: A Case Study of Mu Us Sandy Land

Elucidating the impact of afforestation on soil bacterial community composition and its potential function in afforestation is imperative for comprehending the biochemical processes of land use change. This study employed high-throughput genomic sequencing to determine the bacterial phylogenetic assembly and assess functional groups following afforestation encompassing shrubland and woodland. Compared with non-afforested cropland, the soil organic carbon (SOC) remained unchanged, but significant alterations were observed in the bacterial composition and potential functions under afforestation. Afforestation enhanced bacterial diversity and even shifted the bacteria from the r- to K-strategy, as indicated by higher oligotroph/copiotroph ratios. Soil properties explained 66.45% and 68.9% of the total variation in bacterial community composition at the phylum level and the functional group. A 60.44% decrease in soil water content, a 3.82% increase in pH, a 7.5% increase in bulk density, and a 66.8% decrease in available phosphorus (AP) were the main soil factors affecting both bacterial community composition and functional traits in afforestation. In particular, lower available nutrients, AP, and nitrate nitrogen in afforestation drive the bacterial life history strategies. We conclude that changes in bacterial metabolic functions due to reduced soil available nutrients from dryland afforestation might be the main driver for microbial-inhibited SOC accumulation. These results could provide strong microbiological evidence to help further evaluate the importance of dryland afforestation.

The invasive legume Lupinus polyphyllus has minor site-specific impacts on the composition of soil bacterial communities.

Plant invasions can have major impacts on ecosystems, both above- and belowground. In particular, invasions by legumes, which often host nitrogen-fixing symbionts (rhizobia), are known to modify soil bacterial communities. Here, we examined the effect of the invasive herbaceous legume Lupinus polyphyllus on the alpha diversity and community composition of soil bacteria. We also explored the relationships between these bacterial communities and vegetation cover, the cover of other (non-invasive) legumes, or the number of vascular plants present. For this, we sampled rhizosphere soil and surveyed vegetation from ten paired sites (uninvaded versus invaded more than 10 years ago) in southwestern Finland, and identified bacterial DNA using 16S rRNA gene amplicon sequencing. The presence of the plant invader and the three vegetation variables considered had no effect on the alpha diversity of soil bacteria in terms of bacterial richness or Shannon and Inverse Simpson diversity indices. However, the composition of soil bacterial communities differed between invaded and uninvaded soils at four out of the ten sites. Interestingly, the relative abundances of the top bacterial families in invaded and uninvaded soils were inconsistent across sites, including for legume-associated rhizobia in the family Bradyrhizobiaceae. Other factors-such as vegetation cover, legume cover (excluding L. polyphyllus), number of plant species-also explained a small proportion of the variation in bacterial community composition. Our findings indicate that L. polyphyllus has the potential to modify the composition of local soil bacterial community, at least in sites where it has been present for more than a decade.

Impact of waste separation on the biological nitrogen removal in a MSW incineration leachate treatment plant: Performance and microbial community shift

After waste separation program was launched in China in 2019, incineration leachate treatment plants are facing a challenge of effective removal of nitrogen from leachate due to lack of sufficient carbon source. In this study, the performance of a biological incineration leachate treatment process (anaerobic digestion (AD) - two-stage anoxic/aerobic (A/O) process) was evaluated after adopting the waste separation program, and the changes in the microbial community and function was analyzed using 16S rRNA amplicon sequencing technology. Results showed that after the waste separation, the influent chemical oxygen demand (COD) concentration reduced by 90% (from 19,300 to 1780 mg L−1) with the COD/N ratio decreased from 12.3 to 1.4, which led to a decreased nitrogen removal efficiency (NRE) of <65% and a high effluent NO3− accumulation (445.8–986.5 mg N·L−1). By bypassing approximately 60% of the influent to the two-stage A/O process and adding external carbon source (glucose), the mean NRE increased to 86.3 ± 7.4%. Spearman's analysis revealed that refractory compounds in the bypassed leachate were closely related to the variations in bacterial community composition and nitrogen removal function in the two-stage A/O, leading to a weakened correlation of microbial network. KEGG functional pathway predictions based on Tax4Fun also confirmed that the bypassed leachate induced xenobiotic compounds to the two-stage A/O process, the relative abundance of nitrogen metabolism was reduced by 32%, and more external carbon source was required to ensure the satisfactory nitrogen removal of >80%. The findings provide a good guide for regulation of incineration leachate treatment processes after the waste separation.

Terrestrial dissolved organic matter inputs drive the temporal dynamics of riverine bacterial ecological networks and assembly processes

Rivers receive, transport, and are reactors of terrestrial dissolved organic matter (DOM) and are highly influenced by changes in hydrological conditions and anthropogenic disturbances, but the effect of DOM composition on the dynamics of the bacterial community in rivers is poorly understood. We conducted a seasonal field sampling campaign at two eutrophic river mouth sites to examine how DOM composition influences the temporal dynamics of bacterial community networks, assembly processes, and DOM-bacteria associations. DOM composition and seasonal factors explained 34.7% of the variation in bacterial community composition, and 14.4% was explained purely by DOM composition where specific UV absorbance (SUVA254) as an indicator of aromaticity was the most important predictor. Significant correlations were observed between SUVA254 and the topological features of subnetworks of interspecies and DOM-bacteria associations, indicating that high DOM aromaticity results in more complex and connected networks of bacteria. The bipartite networks between bacterial taxa and DOM molecular formulae (identified by ultrahigh-resolution mass spectrometry) further revealed less specialized bacterial processing of DOM molecular formulae under the conditions of high water level and DOM aromaticity in summer than in winter. A shift in community assembly processes from stronger homogeneous selection in summer to higher stochasticity in winter correlated with changes in DOM composition, and more aromatic DOM was associated with greater similarity in bacterial community composition. Our results highlight the importance of DOM aromaticity as a predictor of the temporal dynamics of riverine bacterial community networks and assembly.

Tree and shrub richness modifies subtropical tree productivity by regulating the diversity and community composition of soil bacteria and archaea

BackgroundDeclines in plant biodiversity often have negative consequences for plant community productivity, and it becomes increasingly acknowledged that this may be driven by shifts in soil microbial communities. So far, the role of fungal communities in driving tree diversity-productivity relationships has been well assessed in forests. However, the role of bacteria and archaea, which are also highly abundant in forest soils and perform pivotal ecosystem functions, has been less investigated in this context. Here, we investigated how tree and shrub richness affects stand-level tree productivity by regulating bacterial and archaeal community diversity and composition. We used a landscape-scale, subtropical tree biodiversity experiment (BEF-China) where tree (1, 2, or 4 species) and shrub richness (0, 2, 4, 8 species) were modified.ResultsOur findings indicated a noteworthy decline in soil bacterial α-diversity as tree species richness increased from monoculture to 2- and 4- tree species mixtures, but a significant increase in archaeal α-diversity. Additionally, we observed that the impact of shrub species richness on microbial α-diversity was largely dependent on the level of tree species richness. The increase in tree species richness greatly reduced the variability in bacterial community composition and the complexity of co-occurrence network, but this effect was marginal for archaea. Both tree and shrub species richness increased the stand-level tree productivity by regulating the diversity and composition of bacterial community and archaeal diversity, with the effects being mediated via increases in soil C:N ratios.ConclusionsOur findings provide insight into the importance of bacterial and archaeal communities in driving the relationship between plant diversity and productivity in subtropical forests and highlight the necessity for a better understanding of prokaryotic communities in forest soils.-4HQdD_EuWHa-cff1NJXs2Video

Semi-arid soil bacterial communities are refined by altered plant selection pressure under conservation management practices

Plants' ability to select for, and refine, their microbiome over time is well known. In soil, the strength of plant selection pressure on microbial composition can result in distinct rhizosphere, and root-zone communities, but may be masked in soils with lower native diversity such as semi-arid soils. Semi-arid soils are also known for their high potential for wind erosion, which may be mitigated by the implementation of cover crops. These cover crops may also alter the microbial composition of the semi-arid soils, but the strength of this effect, and the resulting changes in the composition of the microbiome, are less well known. This study aimed to address whether the implementation of a single-species wheat cover crop in semi-arid agricultural soils would impact the bacterial composition of the cash crop. We investigated three tillage regimes—no-tillage with a winter wheat cover crop, no-tillage winter fallow, and conventional tillage winter fallow—to determine the effects of tillage removal, and cover crop implementation on the soil bacterial community present in the root zone of the cash crop. It was determined that the composition of the bacterial microbiome was similar between cover cropped and non-cover cropped treatments. The similarity of bacterial composition was likely due to the strong effect of environmental selection reducing overall biodiversity in these soils. However, the variability of bacterial community composition was strongly reduced for the cover cropped treatment compared to the two non-cover cropped treatments. The similarity of bacterial communities with cover cropping, without significant soil physicochemical changes, suggests that plant-selection pressure, rather than management-induced changes in soil physicochemical properties, drove the refinement (decreased dissimilarity compared to non-cover cropped treatments) of the bacterial community. The composition of this refined community under cover cropping was determined to contain an enrichment of several genera of interest including N cycling and potential plant-growth promoting bacteria. In summary, the introduction of cover cropping in the nutrient and microbial-poor soil of the semi-arid Southern High Plains strongly refined the bacterial community and selected for organisms with the potential to improve soil functions associated with greater agronomic sustainability.

Inter- and intraspecific phytochemical variation correlate with epiphytic flower and leaf bacterial communities.

Microbes associated with flowers and leaves affect plant health and fitness and modify the chemical phenotypes of plants with consequences for interactions of plants with their environment. However, the drivers of bacterial communities colonizing above-ground parts of grassland plants in the field remain largely unknown. We therefore examined the relationships between phytochemistry and the epiphytic bacterial community composition of flowers and leaves ofRanunculus acris and Trifolium pratense. On 252 plant individuals, we characterized primary and specialized metabolites, that is, surface sugars, volatile organic compounds (VOCs), and metabolic fingerprints, as well as epiphytic flower and leaf bacterial communities. The genomic potential of bacterial colonizers concerning metabolic capacities was assessed using bacterial reference genomes. Phytochemical composition displayed pronounced variation within and between plant species and organs, which explained part of the variation in bacterial community composition. Correlation network analysis suggests strain-specific correlations with metabolites. Analysis of bacterial reference genomes revealed taxon-specific metabolic capabilities that corresponded with genes involved in glycolysis and adaptation to osmotic stress. Our results show relationships between phytochemistry and the flower and leaf bacterial microbiomes suggesting that plants provide chemical niches for distinct bacterial communities. In turn, bacteria may induce alterations in the plants' chemical phenotype. Thus, our study may stimulate further research on the mechanisms of trait-based community assembly in epiphytic bacteria.

Responses of bacterioplankton, particle- and colony-attached bacterial communities to Phaeocystis globosa blooms in Mirs Bay, China

Microalgae blooms are a frequent occurrence in coastal waters worldwide. It is reasonable to assume that these blooms have various influences on bacterial communities, which in turn may affect the development and dissipation of the bloom. However, the bacterial community characteristics, particularly of attached bacteria, associated with microalgae blooms remain unclear. In this study, we investigated the community profiles of bacteria using high-throughput sequencing during a Phaeocystis globosa bloom in Mirs Bay, southern China, in January 2021. Bacteria living in three habitats, i.e., bacterioplankton, particle-attached bacteria, and colony-attached bacteria, were studied from the exponential growth phase to the decline growth phase of the bloom. Distinct variations in bacterial community composition existed among the three habitats. Bacteroidota, Proteobacteria, and Cyanobacteria were the dominant phyla of bacterioplankton, particle–attached bacteria, and colony-attached bacteria, respectively. Richness and diversity were significantly highest (p &amp;lt; 0.01) in particle-attached bacteria, followed by bacterioplankton, and lowest in colony-attached bacteria. The community diversities of bacterioplankton and particle-attached bacteria decreased significantly (p &amp;lt; 0.05) as the bloom shifted from the exponential to the decline phase. During the decline growth phase of the bloom, Bacteroidota and Verrucomicrobiota were the dominant remarkably abundant bacteria in the bacterioplankton community, whereas Verrucomicrobiota was dominant in the particle-attached bacteria community. No significant difference was observed in the colony-attached bacterial community between the exponential and decline phases of the P. globosa bloom owing to their complex network. The results of this study suggest that P. globose bloom has a profound impact on marine bacteria, particularly species that can decompose organic matter, which could play a crucial role in the dissipation of algal blooms.

Soil bacterial community structure in the habitats with different levels of heavy metal pollution at an abandoned polymetallic mine.

Heavy metal pollution caused by mining activities can be harmful to soil microbiota, which are highly sensitive to heavy metal stress. This study aimed to investigate the response of soil bacterial communities to varying levels of heavy metal pollution in four types of habitats (i.e., tailing, remediation, natural recovery, and undisturbed areas) at an abandoned polymetallic mine by high-throughput 16S rRNA gene sequencing, and to determine the dominant ecological processes and major factors driving the variations in bacterial community composition. The diversity and composition of bacterial communities varied significantly between soil habitats (p<0.05). Heterogeneous selection played a crucial role in shaping the difference of bacterial community composition between distinct soil habitats. Redundancy analysis and Pearson correlation analysis revealed that the total contents of Cu and Zn were key factors causing the difference in bacterial community composition in the tailing and remediation areas, whereas bioavailable Mn and Cd, total nitrogen, available nitrogen, soil organic carbon, vegetation coverage, and plant diversity were key factors shaping the soil bacterial structure in the undisturbed and natural recovery areas. These findings provide insights into the distribution patterns of bacterial communities in soil habitats with different levels of heavy metal pollution, and the dominant ecological processes and the corresponding environmental drivers, and expand knowledge in bacterial assembly mechanisms in mining regions.

Alleviation of Cd-polluted paddy soils through Si fertilizer application and its effects on the soil microbial community

In this study, the effects of slag-based Si fertilizers on Cd-polluted paddy soils, soil microbial diversity, and functional properties were evaluated through a long-term field experiment conducted in a double-rice cropping system in southern China. The results showed that soil pH significantly increased from 5.15 to 6.13 after seven years of Si fertilization. Cd accumulation in both the soil and rice plants were significantly decreased for all the Si fertilizers treatments. Treatments using Si fertilizer in powder form exhibited the best alleviation effects, where soil available Cd decreased from 0.50 mg kg−1 to 0.43 mg kg−1, and Cd accumulation in rice roots, straw, and grains decreased by 32.2 %, 57.2 %, and 45.5 %, respectively, than that in the control. Following Si application, the soil microbial richness and Shannon diversity increased from 6731 to 7549 and 7.12 to 7.28, respectively. Proteobacteria, Nitrospirae, and Gemmatimonadetes, were significantly enriched in the Si-treated samples, whereas Verrucomicrobia, Chlamydiia, Ktedonobacteria and Candidatus_Saccharibacteria exhibited opposite patterns. Bioinformatics analysis using phylogenetic investigation of communities by reconstruction of unobserved states tools revealed that the varied microbial community induced functional adaption of soil microorganisms involved in metabolism, genetic information processing, cellular processes, and environmental information processing. The soil pH, NH4-N, and available Cd and Si contents were the key factors that best explained the variations in bacterial community composition among different treatments. Slag-based Si fertilizers are effective for Cd detoxication and can benefit the growth of rice plants throng the regulation of soil microorganisms.

Biogeographical Patterns and Assembly of Bacterial Communities in Saline Soils of Northeast China

Increasing salinity undermines soil fertility and imposes great threats to soil ecosystem productivity and ecological sustainability. Microbes with the ability to adapt to environmental adversity have gained increasing attention for maintenance and restoration of the salt-affected soil ecosystem structure and functioning; however, the characterization of microbial communities in saline–sodic soils remains limited. This study characterized the bacterial community composition and diversity in saline–sodic soils along a latitude gradient across Northeast China, aiming to reveal the mechanism of physicochemical and geographic characteristics shaping the soil bacterial communities. Our results showed that the bacterial community composition and diversity were significantly impacted by soil pH, electrical conductivity, Na+, K+, Cl−, and CO32−. Significant differences in bacterial diversity were revealed along the latitude gradient, and the soil factors accounted for 58.58% of the total variations in bacterial community composition. Proteobacteria, Actinobacteria, Gemmatimonadetes, Chloroflexi, and Bacteroidetes were dominant across all samples. Actinobacteria and Gemmatimonadetes were significantly enriched in high soil sodicity and salinity, while Acidobacteria and Proteobacteria were suppressed by high pH and salt stress in the saline–sodic soils. Increase in soil pH and salinity significantly decreased bacterial species richness and diversity. Community composition analysis indicated that bacterial taxonomic groups (e.g., Bacillus, Egicoccus, Truepera, Halomonas, and Nitrolancea) that may adapt well to high salinity were greatly enriched in the examined soils. The findings collectively evidenced that bacterial community composition and diversity in a broad biographic scale were determined by niche-based environmental characteristics and biotic interactions. The profiling of the soil bacterial communities along the latitude gradient will also provide a basis for a better understanding of the salt-affected soil ecosystem functioning and restoration of these soil ecosystems.

Vertical distribution characteristics and interactions of polycyclic aromatic compounds and bacterial communities in contaminated soil in oil storage tank areas.

Polycyclic aromatic compound (PAC) contamination in soil as a result of oil spills is a serious issue because of the huge global demand for fossil energy. This study assessed the vertical variation in polycyclic aromatic hydrocarbons (PAHs), derivatives of PAHs (dPAHs) and bacterial community structure in deep soil with long-term contamination by oil spillage. Our results suggest that the content of total PACs ranged from 1196.6μg/kg to 14980.9μg/kg and decreased with depth at all sites. PAHs were the most abundant PACs, with a mean concentration of 6640.7μg/kg, followed by oxygenated PAHs (mean 156.3μg/kg) and nitrated PAHs (mean 33.4μg/kg). PAHs are mainly low molecular weight PACs such as naphthalene, fluorene and phenanthrene, while derivatives of PAHs are all low molecular weight PACs and mainly oxygenated PAHs. Low molecular weight PAHs were an important source of dPAHs under specific conditions. The bacterial community structure showed higher bacterial diversity and lower bacterial richness in shallow soil (2-6m in depth) than in deep soil (8-10m in depth). Spearman's analysis confirmed that dramatic bacterial community shifts are a response to contamination. At the genus level, the presence of PACs highly selected for Pseudomonas, belonging to Proteobacteria. Moreover, functional predictions based on Tax4Fun revealed that soil with long-term contamination had a strong potential for PAC degradation. In addition, statistical analysis showed that oxidation-reduction potential (Eh) was closely related to variations of bacterial community composition and function. Finally, Ramlibacter, Pseudomonas, Pseudonocardia, c_MB-A2-108, f_Amb-16S-1323, and Qipengyuania were identified by cooccurrence network analysis as keystone taxa contributing to the maintenance of bacterial ecological function. Together, our results provide evidence of tight bacterial effects of PAHs and dPAHs and a more complete understanding of the fate of PACs in deep contaminated soils.

Novel Interactions Between Phytoplankton and Bacteria Shape Microbial Seasonal Dynamics in Coastal Ocean Waters

Trophic interactions between marine phytoplankton and heterotrophic bacteria are at the base of the biogeochemical carbon cycling in the ocean. However, the specific interactions taking place between phytoplankton and bacterial taxa remain largely unexplored, particularly out of phytoplankton blooming events. Here, we applied network analysis to a 3.5-year time-series dataset to assess the specific associations between different phytoplankton and bacterial taxa along the seasonal scale, distinguishing between free-living and particle-attached bacteria. Using a newly developed network post-analysis technique we removed bacteria-phytoplankton correlations that were primarily driven by environmental parameters, to detect potential biotic interactions. Our results indicate that phytoplankton dynamics may be a strong driver of the inter-annual variability in bacterial community composition. We found the highest abundance of specific bacteria-phytoplankton associations in the particle-attached fraction, indicating a tighter bacteria-phytoplankton association than in the free-living fraction. In the particle-associated fraction we unveiled novel potential associations such as the one between Planctomycetes taxa and the diatom Leptocylindrus spp. Consistent correlations were also found between free-living bacterial taxa and different diatoms, including novel associations such as those between SAR11 with Naviculales diatom order, and between Actinobacteria and Cylindrotheca spp. We also confirmed previously known associations between Rhodobacteraceae and Thalassiosira spp. Our results expand our view on bacteria-phytoplankton associations, suggesting that taxa-specific interactions may largely impact the seasonal dynamics of heterotrophic bacterial communities.

Time after time: detecting annual patterns in stream bacterial biofilm communities.

SummaryTo quantify the major environmental drivers of stream bacterial population dynamics, we modelled temporal differences in stream bacterial communities to quantify community shifts, including those relating to cyclical seasonal variation and more sporadic bloom events. We applied Illumina MiSeq 16S rRNA bacterial gene sequencing of 892 stream biofilm samples, collected monthly for 36‐months from six streams. The streams were located a maximum of 118 km apart and drained three different catchment types (forest, urban and rural land uses). We identified repeatable seasonal patterns among bacterial taxa, allowing their separation into three ecological groupings, those following linear, bloom/trough and repeated, seasonal trends. Various physicochemical parameters (light, water and air temperature, pH, dissolved oxygen, nutrients) were linked to temporal community changes. Our models indicate that bloom events and seasonal episodes modify biofilm bacterial populations, suggesting that distinct microbial taxa thrive during these events including non‐cyanobacterial community members. These models could aid in determining how temporal environmental changes affect community assembly and guide the selection of appropriate statistical models to capture future community responses to environmental change.

The bacterial community of childcare centers: potential implications for microbial dispersal and child exposure

BackgroundBacterial communities within built environments reflect differences in sources of bacteria, building design, and environmental contexts. These communities impact the health of their occupants in many ways. Children interact with the built environment differently than do adults as a result of their unique behaviors, size, and developmental status. Consequently, understanding the broader bacterial community to which children are exposed will help inform public health efforts and contribute to our growing understanding of the bacterial community associated with childcare centers.MethodsWe sampled childcare centers to survey the variation in bacterial community composition across five surfaces found inside and outside twelve classrooms and six centers using 16S rRNA marker gene amplicon sequencing. We then correlated these bacterial community analyses of surfaces with environmental and demographic measures of illumination and classroom occupant density.ResultsThe childcare environment was dominated by human-associated bacteria with modest input from outdoor sources. Though the bacterial communities of individual childcare centers differed, there was a greater difference in the bacterial community within a classroom than among centers. Surface habitats—fomites—within the classroom, did not differ in community composition despite differing proximity to likely sources of bacteria, and possible environmental filters, such as light. Bacterial communities did correlate with occupant density and differed significantly between high and low usage surfaces.ConclusionsOur results suggest built environments inhabited by young children are similar to functionally equivalent built environments inhabited by adults, despite the different way young children engage with their environment. Ultimately, these results will be useful when further interrogating microbial dispersal and human exposure to microorganisms in built environments that specifically cater to young children.

Vertical Microbial Profiling of Arabian Sea Oxygen Minimal Zone Reveals Complex Bacterial Communities and Distinct Functional Implications.

Arabian Sea harbours one of the largest oxygen minimal zones (OMZs) among the global oceans wherein biogeochemical cycles are regulated through dominant and complex microbial processes. The present study investigated the bacterial communities at various depths of the Arabian Sea OMZ using high-throughput sequencing of the v3-v4 hyper variable region of 16S rRNA gene. A total of 10 samples which included water samples from 8 different depths and 2 sediment samples were analyzed in this study. About 2.7 million sequences were obtained from all the samples. The sequence analysis revealed high bacterial diversity at deep waters and sediment samples and comparatively less species richness at the core OMZ depths. Number of OTUs ranged from 114 to 14441.Taxonomic assignments of the obtained OTUs showed dominant presence of Proteobacteria, Bacteriodetes, and Chloroflexi across all the samples. The identified OTUs were further affiliated to the phyla Marinimicrobia, Colwellia, Nitrospina, Tepidicaulis, Shewanella, Pseudoalteromonas, Woeseia at various depths along the water column. Correlation with abiotic factors suggested distinct variation in bacterial community composition with change in depth and dissolved oxygen (DO) levels. Predictive functional annotation based on bacterial phylotypes suggested presence of active nitrogen, sulphur, carbon, and methane metabolic cycles along the vertical transect of the studied region. Presence of nitrogen reduction bacterial group below the core OMZ depths may potentially provide insight into the expansion of OMZ region in Arabian Sea. Functional profiling further revealed presence of genes related to xenobiotic degradation in the water and sediment samples indicating a potential hotspot for bio-prospection.

Bacterial diversity and community composition in lake water and sediment of Lake Daihai

采用高通量测序技术，研究了内蒙古岱海流域入湖河流、湖水及沉积物细菌多样性及群落组成.结果显示，细菌多样性从高到低依次为：沉积物>河流>湖泊.聚类分析表明入湖河流、湖水和沉积物细菌群落可分为明显不同的3支，说明这3种生境中细菌群落结构有较大差异.物种注释结果表明，河流中优势细菌菌群为髌骨细菌（Patescibacteria）、变形菌门（Proteobacteria）、拟杆菌门（Bacteroidetes）和放线菌门（Actinobacteria）；湖水中优势细菌菌群为放线菌门（Actinobacteria）；而沉积物中优势细菌菌群为变形菌门和绿弯菌门（Chloroflexi）.典范对应分析及Monte Carlo检验表明，电导率和悬浮物含量对水体中（河流与湖泊）细菌群落影响显著，二者共解释了细菌群落变化的86.5%；而冗余分析及Monte Carlo检验表明，泥深、磁化率和总有机碳对沉积物中细菌群落影响显著，三者共解释了细菌群落变化的47.9%.近30年来，岱海地区气候变化和人类活动导致湖水咸化，沉积物碳氮指标显著增长.岱海水体及沉积物细菌多样性及群落组成的差异及其主要驱动因子，反映了细菌对这种气候变化和人类活动共同作用的响应.;Bacterial diversity and community composition was investigated in the Lake Daihai Basin, Inner Mongolia using high-throughput sequencing technology. The results showed that bacterial diversity was highest in sediments, followed by river and lake water. Cluster analysis showed that bacterial community compositions in the inflowing river, lake water and sediments were separated into three distinct groups, indicating great differences in bacterial community compositions among the three habitats. Taxonomic annotation showed that the dominant bacterial flora in the river was Patescibacteria, Proteobacteria, Bacteroidetes and Actinobacteria. Actinobacteria was the most dominant bacteria phylum in the lake water, while the dominant bacterial flora in sediments were Proteobacteria and Chloroflexi. Canonical correspondence analysis and Monte Carlo permutation test revealed that the variations of bacterial community compositions in the river and lake were significantly explained by conductivity and suspended solids, which explained 86.5% of the variation. Redundant analysis and Monte Carlo permutation test revealed that the variations of bacterial community compositions in sediment were significantly explained by depth, magnetic susceptibility and total organic carbon, which explained 47.9% of the variation in total. During the past 30 years, Lake Daihai has experienced salinization in lake water and a remarkable increase of carbon and nitrogen in the sediment due to climate change and anthropogenic activities. The variations of bacterial diversity and community composition in the water and sediments, as well as their main driving environmental factors, highlight the responses of bacteria to the combined effects of climate change and anthropogenic activities on Lake Daihai.

Long-term fertilization and tillage regimes have limited effects on structuring bacterial and denitrifier communities in a sandy loam UK soil.

Denitrification causes loss of available nitrogen from soil systems, thereby reducing crop productivity and increasing reliance on agrochemicals. The dynamics of denitrification and denitrifying communities are thought to be altered by land management practices, which affect the physicochemical properties of the soil. In this study, we look at the effects of long-term tillage and fertilization regimes on arable soils following 16 years of treatment in a factorial field trial. By studying the bacterial community composition based on 16S rRNA amplicons, absolute bacterial abundance and diversity of denitrification functional genes (nirK, nirS and nosZ), under conditions of minimum/conventional tillage and organic/synthetic mineral fertilizer, we tested how specific land management histories affect the diversity and distribution of both bacteria and denitrification genes. Bacterial and denitrifier communities were largely unaffected by land management history and clustered predominantly by spatial location, indicating that the variability in bacterial community composition in these arable soils is governed by innate environmental differences and Euclidean distance rather than agricultural management intervention.