Distribution Of Bacterial Communities Research Articles

Vertical distribution of size-fractionated bacterial communities in the water column of the Atacama Trench

Variation of vertical distribution of bacterial communities through the whole water column of the trench regions has received more and more attention. However, it is still unclear whether there are unique microbial communities in trenches. The study investigated the bacterial composition and diversity in three size-fractions (0.3-0.7μm, 0.7–2.7μm, and >3μm) from the surface to the hadal zone (7500 m) at one site in the Atacama Trench. The results showed that the alpha diversity changed with depth and was the highest at 6000 m and lowest at 1000 m. For different size fractions, the bacterial diversity was higher in 0.7-2.7μm and >2.7μm fractions than 0.3-0.7μm in the surface water, but the diversity in 0.3-0.7μm fraction was the highest in the hadalpelagic, likely reflecting the depth changes of quantity and bioavailability of organic matter. Firmicutes were the most abundant bacteria (36.3 ± 15.6%) in the water depth, while Alphaproteobacteria dominated in the samples at 7500 m for the 0.3–0.7μm fraction (36.3%), and 7000–7500 m for the 0.7–2.7μm fraction (30.6 ± 1.2%). PCoA analysis indicated that the hadalpelagic bacterial communities were more like those in the overlying deep water, but were distinct from the epipelagic in the study area. Though no significant differences among size fractions of bacterial community were observed in the pelagic Atacama Trench, lifestyle preferences existed that some relied on particulate matter, and some preferred to live freely. This suggested the important influence of surface primary production and export production on the bacterial communities in the deep ocean.

The Depletion Mechanism Actuates Bacterial Aggregation by Exopolysaccharides and Determines Species Distribution & Composition in Bacterial Aggregates.

Bacteria in natural environments and infections are often found in cell aggregates suspended in polymer-rich solutions, and aggregation can promote bacterial survival and stress resistance. One aggregation mechanism, called depletion aggregation, is driven by physical forces between bacteria and high concentrations of polymers in the environment rather than bacterial activity per se. As such, bacteria aggregated by the depletion mechanism will disperse when polymer concentrations fall unless other adhesion mechanisms supervene. Here we investigated whether the depletion mechanism can actuate the aggregating effects of Pseudomonas aeruginosa exopolysaccharides for suspended (i.e. not surface attached) bacteria, and how depletion affects bacterial inter-species interactions. We found that cells overexpressing the exopolysaccharides Pel and Psl remained aggregated after short periods of depletion aggregation whereas wild-type and mucoid P. aeruginosa did not. In co-culture, depletion aggregation had contrasting effects on P. aeruginosa’s interactions with coccus- and rod-shaped bacteria. Depletion caused S. aureus (cocci) and P. aeruginosa (rods) to segregate from each other and S. aureus to resist secreted P. aeruginosa antimicrobial factors resulting in species co-existence. In contrast, depletion aggregation caused P. aeruginosa and Burkholderia sp. (both rods) to intermix, enhancing type VI secretion inhibition of Burkholderia by P. aeruginosa, leading to P. aeruginosa dominance. These results show that in addition to being a primary cause of aggregation in polymer-rich suspensions, physical forces inherent to the depletion mechanism can promote aggregation by some self-produced exopolysaccharides and determine species distribution and composition of bacterial communities.

Physical Process Controlling the Surface Bacterial Community Composition in the Ulleung Basin of East Sea

Although environmental drivers are known to shape the abundance and distribution of bacterial communities in the East Sea, the effects of physical processes have not been directly studied. Here, we aimed to examine the influences of water mass mixing (summer) and eddy circulation (winter) on the surface bacterial communities of the Ulleung Basin (UB), East Sea, based on the metagenomic approach. Overall, 490,087 operational taxonomic units (OTUs) were identified from five stations, and prokaryotic abundance was dominant at all stations in both seasons. Among the prokaryotes, most OTUs were affiliated with Proteobacteria, Cyanobacteria, Flavobacteria, and Actinobacteria during summer and winter. Bacterial communities were found to differ with water masses (Changjiang, Tsushima, and North Korea surface water) and eddy circulation, and were strongly correlated with environmental variables, suggesting specific bacterial community responses with specific seasonal physicochemical parameters. Our investigation indicates that together with distance and environment, advection shapes the UB bacterial community composition, helping us better understand the physical cues related to biological composition in the East Sea. However, further studies are needed to ascertain the role of microbial functional genes along with the advection of oceanographic processes in the East Sea to better understand the regional biogeochemical processes.

Abundant and rare bacteria possess different diversity and function in crop monoculture and rotation systems across regional farmland

Revealing regional distribution and diversity of abundant and rare bacterial communities in different cropping systems are crucial to predict trends of microbial changes in farmlands and understand ecosystem functions. Here, we examined the spatial distribution patterns and calculated differences in diversity and function for abundant and rare bacterial sub-communities across 114 typical dryland farmland (corn, soybean and alfalfa) soils in crop monoculture (CM) and rotation (CR) systems in northeastern China. Significant (P < 0.001) distance-decay relationships were detected for the abundant and rare sub-communities in both CM and CR systems. In addition, edaphic variables (CMabundant = 27.3%, CMrare = 9.1%; CRabundant = 33.3%, CRrare = 15.3%) largely contributed to the variation of sub-communities based on variance partitioning analysis (VPA). Shannon and Chao1 indices were significantly (P < 0.05) different between abundant and rare sub-communities in CM and CR systems. Both abundant (RANOSIM = 0.065, P = 0.004) and rare (RANOSIM = 0.054, P = 0.013) bacterial community were significantly (P < 0.05) separated according to CM and CR systems. Based on Tax4Fun, for Proteobacteria, environmental information processing was the main potential function in CM, while metabolism was the one in CR system. Additionally, the potential functions of rare taxa were greater than that of abundant taxa both in CM and CR systems. Our results would not only provide theoretical support for better understanding the roles of rare and abundant bacteria, but also offered new opportunity to improve agricultural ecosystem functions.

Characteristics of soil carbon emissions and bacterial community composition in peatlands at different stages of vegetation succession

Microorganisms are important components of soil ecosystems and play an important role in material cycles. Northern peatlands are important ecosystems in middle-high latitude regions. In peatlands, different vegetation successions occur with changes in groundwater levels. The overall carbon emission of peat bogs is related to the carbon stability of the surrounding environment. Unraveling the assembly and distribution of bacterial communities at different succession stages in peatland is essential to understanding the soil nutrient cycle. In this study, we investigated the characteristics of soil carbon emissions and the composition of subsurface microorganisms under six different succession stages. The highest carbon emission was observed in mossy peatlands, and their soil enzyme activity was closely related to the aboveground vegetation cover type. The succession pattern of ground vegetation was the main driver of soil microorganisms. The abundance of the dominant Proteobacteria decreased with increasing soil depth, while the opposite trend was observed for Chloroflexi. Furthermore, the community structure of microorganisms became progressively simpler and looser as soil water content decreased. The bacterial alpha diversity was driven by soil dissolved organic carbon and Fe, and the beta diversity was driven mainly by soil water content. The bacteria presented a random distribution in a nutrient-rich soil environment and shifted to deterministic distribution with decreasing water and nutrient contents. The balance between taxonomic diversity and dispersal limitation mediates species coexistence in the soil microbiome. This study provides new insights into the soil environment at different stages of succession in peatlands.

Bacterial Communities and Culturable Petroleum Hydrocarbon Degrading Bacteria in Marine Sediments in the Northeastern South China Sea

Marine oil spill pollution was one of the factors affecting the marine ecology of the northeastern South China Sea (nSCS). The submarine oil produced after the oil spill had a long-term impact on the microbial community in the sediment. In this study, 16S rRNA genes high-throughput sequencing and quantitative PCR were used to study the composition and distribution of bacterial communities in deep-sea sediments; meanwhile, petroleum hydrocarbon degrading bacteria were isolated, of which activity were detected. Proteobacteria and Planctomycetota were the main bacterial phyla found in the samples studied in this study. 29 bacterial strains capable of degrading petroleum hydrocarbons were isolated from S02 and S39 sediment samples, belonging to genus Stenotrophomonas, Pseudidiomarina, Sulfitobacter, Pseudomonas, Halomonas and so on. Strains from Stenotrophomonas degraded petroleum hydrocarbons efficiently. This research provided new insights into distribution pattern of benthic microbial community in the nSCS, and validated the degradation potential of petroleum hydrocarbons by indigenous bacteria.

Metagenomic investigation of the seasonal distribution of bacterial community and antibiotic-resistant genes in Day River Downstream, Ninh Binh, Vietnam

In this study, we use high-throughput sequencing-based metagenomic methods to investigate the differences in seasonal structures of the bacterial community and the abundance and diversity of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in both shrimp ponds and river water samples downstream of the Day River, Ninh Binh, Vietnam. The structure of the central bacterial community, ARGs, and MGEs was found to be regardless of the seasons and locations. The predominant phyla found in all samples was Proteobacteria, Bacteroidetes, and Actinobacteria. Multi-drug resistance (MDR) genes and transposases are the most dominant ARG types and MGEs, respectively. Our data showed a higher abundance of bacterial communities, ARGs, and MGEs in the river water during the rainy season. There is a significant correlation between the abundance of ARGs, MGEs, and environmental factors. Our results indicate that water environments containing ARGs/MGEs carrying bacteria pose a risk to shrimp and human health, especially during the rainfall-polluted water season.

Water Mass Controlled Vertical Stratification of Bacterial and Archaeal Communities in the Western Arctic Ocean During Summer Sea-Ice Melting.

The environmental variations and their interactions with the biosphere are vital in the Arctic Ocean during the summer sea-ice melting period in the current scenario of climate change. Hence, we analysed the vertical distribution of bacterial and archaeal communities in the western Arctic Ocean from sea surface melt-ponds to deep water up to a 3040 m depth. The distribution of microbial communities showed a clear stratification with significant differences among different water depths, and the water masses in the Arctic Ocean - surface mixed layer, Atlantic water mass and deep Arctic water - appeared as a major factor explaining their distribution in the water column. A total of 34 bacterial phyla were detected in the seawater and 10 bacterial phyla in melt-ponds. Proteobacteria was the dominant phyla in the seawater irrespective of depth, whereas Bacteroidota was the dominant phyla in the melt-ponds. A fast expectation-maximization microbial source tracking analysis revealed that only limited dispersion of the bacterial community was possible across the stratified water column. The surface water mass contributed 21% of the microbial community to the deep chlorophyll maximum (DCM), while the DCM waters contributed only 3% of the microbial communities to the deeper water masses. Atlantic water mass contributed 37% to the microbial community of the deep Arctic water. Oligotrophic heterotrophic bacteria were dominant in the melt-ponds and surface waters, whereas chemoautotrophic and mixotrophic bacterial and archaeal communities were abundant in deeper waters. Chlorophyll and ammonium were the major environmental factors that determined the surface microbial communities, whereas inorganic nutrient concentrations controlled the deep-water communities.

Diversity and Vertical Distribution of Sedimentary Bacterial Communities and Its Association with Metal Bioavailability in Three Distinct Mangrove Reserves of South China

The structure of sedimentary bacterial communities in mangroves depends on environmental factors such as pH, salinity, organic matter content, and metal pollution. To investigate the effect of heavy metal pollution on such communities, core samples of sediments from four sites in three distinct mangrove reserves (Golden Bay Mangrove Reserve in Beihai, Guangxi province (GXJHW), Shankou Mangrove Reserve in Hepu, Guangxi province (GXSK), and MaiPo mangrove in Hong Kong (MPCT and MPFQ)) in South China were analyzed for physicochemical properties, multiple chemical forms of metals, and vertical bacterial diversity. Sedimentary bacterial communities varied greatly among the different sampling sites, with biodiversity decreasing in the order of GXSK, GXJHW, MPFQ, and MPCT. Proteobacteria was the dominant phylum, followed by Chloroflexi, across all four sampling sites. Multivariate statistical analysis of the effect of environmental factors on the sedimentary bacterial communities found that total carbon was the only physicochemical factor with a significant influence at all four sites. The correlations between environmental factors and bacterial structure were weak for the two sites in Guangxi province, but strong at MPCT in Hong Kong where environmental factors were almost all significantly negatively correlated with bacterial diversity. Variance partitioning analysis revealed that physicochemical properties and chemical forms of metals could explain most of the changes in bacterial diversity. Overall, we observed that heavy metal forms were more important than total metal content in influencing the sedimentary bacterial diversity in mangroves, consistent with the more bioavailable metal species having the greatest effect.

The overlap of soil and vegetable microbes drives the transfer of antibiotic resistance genes from manure-amended soil to vegetables

Livestock manure, as a major source of antibiotic resistance genes (ARGs), could further transfer ARGs from soil to vegetables when it's used as fertilizer in field and then pose threat to human health. Meanwhile, manure inputs and vegetable planting also affect soil bacterial communities, but these effects on the transmission of ARGs from soil to vegetable is still lacking. Here, lettuce and endive were cultivated in manure-amended soils using pot experiment. The distribution of bacterial community, ARGs and intI1 gene were studied in manure-amended soil and vegetable roots and leaves at harvest. High-throughput sequencing analysis demonstrated that planting vegetables exerted significant effect on soil bacterial communities, which partly explained the decrease of certain ARGs and the intI1 gene in planted soil than in control soil. ARGs in vegetable and soil were interconnected. The bacterial community compositions among root endophyte, leaf endophyte, and phyllosphere were varied by Hierarchical clustering analysis. Higher abundance of shared bacterial taxa was found between root endophytes and soil microbes, which could lead to a relative higher detection frequency of ARGs in root endophyte. Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes were dominant in the plant endophyte and phyllosphere microbes and had intensive correlations with ARGs. Taken together, our findings provided valuable insights into the role of bacterial community structure in the dissemination of ARGs from manure-amended soil to vegetables.

Estimating soil bacterial abundance and diversity in the Southeast Qinghai-Tibet Plateau

Soil bacteria play important functional roles in ecosystems but are challenging to investigate because of time-consuming and costly laboratory analyses. Digital soil mapping (DSM) technology is an emerging and efficient tool for regionalization of soil bacteria. It has been introduced as a viable complementary approach to the traditional methods for expression of the spatial distribution of soil properties due to being fast and cost-effective. This study was conducted to develop a strategy for mapping the relative abundance of the dominant phyla and community diversities of bacteria to have a better understanding of their biogeography in the highly heterogeneous area of Southeast Tibet, China. Here, we developed state-factor models using predictor variables that were already mapped and publicly available soil and environmental proxies for edaphic, climatic, biotic and topographic factors. We evaluated seven statistical and machine learning algorithms; namely, partial least squares regression (PLSR), random forest (RF), Cubist, support vector machines (SVM), Gaussian process regression (GPR), XG-boost (XGB) and convolutional neural networks (CNNs). Ten-fold cross-validation with all observations revealed that the CNNs outperformed other algorithms and could explain between 48% and 72% of the variation in bacterial abundance and diversity. Estimates of the relative abundance of Actinobacteria and Proteobacteria produced the largest R2 values (≥0.70), while estimates of Acidobacteria, Gemmatimonadetes, Chloroflexi, and Planctomycetes produced values of 0.6 ≤ R2 < 0.7, and estimates of Verrucomicrobia, Bacteroidetes, Nitrospirae, OTUs, and Shannon diversity produced values of 0.5 ≤ R2 < 0.6. The estimates for Firmicutes were poorest, with R2 values < 0.5. The estimated phyla abundances and diversities clearly exhibited regional patterns and local characteristics. Soil total nitrogen (TN), carbon to nitrogen ratio (C/N), pH, clay content, and temperature were prominent controls that regulated bacterial community distribution.

The Role of Environmental Processes and Geographic Distance in Regulating Local and Regionally Abundant and Rare Bacterioplankton in Lakes.

Bacteria are vital components of lake systems, driving a variety of biogeochemical cycles and ecosystem services. Bacterial communities have been shown to have a skewed distribution with a few abundant species and a large number of rare species. The contribution of environmental processes or geographic distance in structuring these components is uncertain. The discrete nature of lakes provides an ideal test case to investigate microbial biogeographical patterns. In the present study, we used 16S rRNA gene metabarcoding to examine the distribution patterns on local and regional scales of abundant and rare planktonic bacteria across 167 New Zealand lakes covering broad environmental gradients. Only a few amplicon sequence variants (ASVs) were abundant with a higher proportion of rare ASVs. The proportion of locally abundant ASVs was negatively correlated with the percentage of high productivity grassland in the catchment and positively with altitude. Regionally rare ASVs had a restricted distribution and were only found in one or a few lakes. In general, regionally abundant ASVs had higher occupancy rates, although there were some with restricted occupancy. Environmental processes made a higher contribution to structuring the regionally abundant community, while geographic distances were more important for regionally rare ASVs. A better understanding of the processes structuring the abundance and distribution of bacterial communities within lakes will assist in understand microbial biogeography and in predicting how these communities might shift with environmental change.

Soil pH: a key edaphic factor regulating distribution and functions of bacterial community along vertical soil profiles in red soil of pomelo orchard

BackgroundSoil microbes exist throughout the soil profile and those inhabiting topsoil (0–20 cm) are believed to play a key role in nutrients cycling. However, the majority of the soil microbiology studies have exclusively focused on the distribution of soil microbial communities in the topsoil, and it remains poorly understood through the subsurface soil profile (i.e., 20–40 and 40–60 cm). Here, we examined how the bacterial community composition and functional diversity changes under intensive fertilization across vertical soil profiles [(0–20 cm (RS1), 20–40 cm (RS2), and 40–60 cm (RS3)] in the red soil of pomelo orchard, Pinghe County, Fujian, China.ResultsBacterial community composition was determined by 16S rRNA gene sequencing and interlinked with edaphic factors, including soil pH, available phosphorous (AP), available nitrogen (AN), and available potassium (AK) to investigate the key edaphic factors that shape the soil bacterial community along with different soil profiles. The most dominant bacterial taxa were Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Crenarchaeota, and Bacteriodetes. Bacterial richness and diversity was highest in RS1 and declined with increasing soil depth. The distinct distribution patterns of the bacterial community were found across the different soil profiles. Besides, soil pH exhibited a strong influence (pH ˃AP ˃AN) on the bacterial communities under all soil depths. The relative abundance of Proteobacteria, Actinobacteria, Crenarchaeota, and Firmicutes was negatively correlated with soil pH, while Acidobacteria, Chloroflexi, Bacteriodetes, Planctomycetes, and Gemmatimonadetes were positively correlated with soil pH. Co-occurrence network analysis revealed that network topological features were weakened with increasing soil depth, indicating a more stable bacterial community in the RS1. Bacterial functions were estimated using FAPROTAX and the relative abundance of functional bacterial community related to metabolic processes, including C-cycle, N-cycle, and energy production was significantly higher in RS1 compared to RS2 and RS3, and soil pH had a significant effect on these functional microbes.ConclusionsThis study provided the valuable findings regarding the structure and functions of bacterial communities in red soil of pomelo orchards, and highlighted the importance of soil depth and pH in shaping the soil bacterial population, their spatial distribution and ecological functioning. These results suggest the alleviation of soil acidification by adopting integrated management practices to preserve the soil microbial communities for better ecological functioning.

Effects of different types of anthropogenic disturbances and natural wetlands on water quality and microbial communities in a typical black-odor river

Natural rivers have always been invaded by multiple pollutants discharged by anthropogenic activities, inducing physiochemical and biological changes to waterbodies. However, the effects of different types of anthropogenic disturbances and natural wetlands on water quality and bacterial communities in black-odor rivers remain largely unknown. In this study, 13 water quality parameters at 48 sampling sites along the typical contaminated Jishan River were selected to evaluate water quality through water quality index (WQI). The analysis of microbial community composition and its correlation with water quality of different disturbances (industrial effluent, aquacultural wastewater, domestic sewage, confluences, dam and wetlands) were further conducted. The results revealed that water quality parameters had significant spatial heterogeneity in water samples of different disturbed sites, and the different types of disturbances shaped the abundance and distribution of bacterial communities. Among these disturbances, dam altered the hydrological and hydraulic conditions of this river, leading to the worst water quality, with the fermentative microorganism Lactococcus becoming the dominant genus. Natural wetlands surrounding the terminus of this river had recuperative functions and could restore water quality and microbial community. The WQI values 38.08–63.46 were rated as “low” or “moderate” and primarily affected by excessive nutrient contaminates, such as nitrogen, phosphorus, and organic matter. Random forest analysis revealed that the biomarkers for water quality were C39, Trichococcus, norank_f_norank_o_Chloroplast, and unclassified_f_Enterobacteriaceae. This study not only facilitated a more comprehensive understanding about the correlation between water quality and bacterial communities of river ecosystem but also provided theoretical support for ecological restoration and governmental regulation of the water ecosystem.

Vertical Distribution of Soil Bacterial Communities in Different Forest Types Along an Elevation Gradient.

Microorganisms inhabit the entire soil profile and play important roles in nutrient cycling and soil formation. Recent studies have found that soil bacterial diversity and composition differ significantly among soil layers. However, little is known about the vertical variation in soil bacterial communities and how it may change along an elevation gradient. In this study, we collected soil samples from 5 forest types along an elevation gradient in Taibai Mountain to characterize the bacterial communities and their vertical patterns and variations across soil profiles. The richness and Shannon index of soil bacterial communities decreased from surface soils to deep soils in three forest types, and were comparable among soil layers in the other two forests at the medium elevation. The composition of soil bacterial communities differed significantly between soil layers in all forest types, and was primarily affected by soil C availability. Oligotrophic members of the bacterial taxa, such as Chloroflexi, Gemmatimonadetes, Nitrospirae, and AD3, were more abundant in the deep layers. The assembly of soil bacterial communities within each soil profile was mainly governed by deterministic processes based on environmental heterogeneity. The vertical variations in soil bacterial communities differed among forest types, and the soil bacterial communities in the Betula albo-sinensis forest at the medium elevation had the lowest vertical variation. The vertical variation was negatively correlated with mean annual precipitation (MAP), weighted rock content, and weighted sand particle content in soils, among which MAP had the highest explanatory power. These results indicated that the vertical mobilization of microbes with preferential and matrix flows likely enhanced bacterial homogeneity. Overall, our results suggest that the vertical variations in soil bacterial communities differ along the elevation gradient and potentially affect soil biological processes across soil profiles.

Diversity and Distribution of Anaerobic Ammonium Oxidation Bacteria in Hot Springs of Conghua, China.

Anaerobic ammonium oxidation (anammox) is an important process of the nitrogen cycle, and the anammox bacteria have been studied in a wide variety of environments. However, the distribution, diversity, and abundance of anammox bacteria in hot springs remain enigmatic. In this study, the anammox process was firstly investigated in hot springs of Conghua, China. Anammox-like bacterial sequences that closely affiliated to “Candidatus Brocadia,” “Candidatus Kuenenia,” “Candidatus Scalindua,” “Candidatus Anammoxoglobus,” and “Candidatus Jettenia” were detected. Several operational taxonomic units (OTUs) from this study shared low sequence identities to the 16S rRNA gene of the known anammox bacteria, suggesting that they might be representing putative novel anammox bacteria. A quantitative PCR analysis of anammox-specific 16S rRNA gene confirmed that the abundance of anammox bacteria ranged from 1.60 × 104 to 1.20 × 107 copies L–1. Nitrate was a key environmental factor defining the geographical distribution of the anammox bacterial community in the hot spring ecosystem. Dissolved inorganic carbon had a significant influence on anammox bacterial biodiversity. Our findings for the first time revealed that the diverse anammox bacteria, including putative novel anammox bacterial candidates, were present in Conghua hot spring, which extended the existence of anammox bacteria to the hot springs in China and expands our knowledge of the biogeography of anammox bacteria. This work filled up the research lacuna of anammox bacteria in Chinese hot spring habitat and would guide for enrichment strategies of anammox bacteria of Conghua hot springs.

Spatial Distribution of the Pepper Blight (Phytophthora capsici) Suppressive Microbiome in the Rhizosphere.

The properties of plant rhizosphere are dynamic and heterogeneous, serving as different habitat filters for or against certain microorganisms. Herein, we studied the spatial distribution of bacterial communities in the rhizosphere of pepper plants treated with a disease-suppressive or non-suppressive soil. The bacterial richness was significantly (p < 0.05) higher in plants treated with the disease-suppressive soil than in those treated with the non-suppressive soil. Bacterial richness and evenness greatly differed between root parts, with decrease from the upper taproot to the upper fibrous root, the lower taproot, and the lower fibrous root. As expected, the bacterial community in the rhizosphere differed between suppressive and non-suppressive soil. However, the spatial variation (36%) of the bacterial community in the rhizosphere was much greater than that explained by soils (10%). Taxa such as subgroups of Acidobacteria, Nitrosospira, and Nitrospira were known to be selectively enriched in the upper taproot. In vitro Bacillus antagonists against Phytophthora capsici were also preferentially colonized in the taproot, while the genera such as Clostridium, Rhizobium, Azotobacter, Hydrogenophaga, and Magnetospirillum were enriched in the lower taproot or fibrous root. In conclusion, the spatial distribution of bacterial taxa and antagonists in the rhizosphere of pepper sheds light on our understanding of microbial ecology in the rhizosphere.

Vertical distribution patterns and drivers of soil bacterial communities across the continuous permafrost region of northeastern China

BackgroundSoil microorganisms in the thawing permafrost play key roles in the maintenance of ecosystem function and regulation of biogeochemical cycles. However, our knowledge of patterns and drivers of permafrost microbial communities is limited in northeastern China. Therefore, we investigated the community structure of soil bacteria in the active, transition and permafrost layers based on 90 soil samples collected from 10 sites across the continuous permafrost region using high-throughput Illumina sequencing.ResultsProteobacteria (31.59%), Acidobacteria (18.63%), Bacteroidetes (9.74%), Chloroflexi (7.01%) and Actinobacteria (6.92%) were the predominant phyla of the bacterial community in all soil layers; however, the relative abundances of the dominant bacterial taxa varied with soil depth. The bacterial community alpha-diversity based on the Shannon index and the phylogenetic diversity index both decreased significantly with depth across the transition from active layer to permafrost layer. Nonmetric multidimensional scaling analysis and permutation multivariate analysis of variance revealed that microbial community structures were significantly different among layers. Redundancy analysis and Spearman’s correlation analysis showed that soil properties differed between layers such as soil nutrient content, temperature and moisture mainly drove the differentiation of bacterial communities.ConclusionsOur results revealed significant differences in bacterial composition and diversity among soil layers. Our findings suggest that the heterogeneous environmental conditions between the three soil horizons had strong influences on microbial niche differentiation and further explained the variability of soil bacterial community structures. This effort to profile the vertical distribution of bacterial communities may enable better evaluations of changes in microbial dynamics in response to permafrost thaw, which would be beneficial to ecological conservation of permafrost ecosystems.

Spatial and Temporal Distribution of Aerobic Denitrification Bacterial Community in Sediments of Gangnan Reservoir

In order to study the spatial and temporal distribution characteristics of aerobic denitrification bacteria in the sediments of Gangnan Reservoir, the aerobic denitrification bacterial community was analyzed using a MiSeq high-throughput sequencing technique based on the napA gene. Moreover, the composition, diversity, difference, and network analysis of the aerobic denitrification bacterial community were investigated. The results showed higher α-diversity (Chao1 index, Observed species index, and Shannon index) in autumn and winter than that in spring and summer; that is, the richness and diversity of sampling sites in autumn and winter were higher. In terms of spatial distribution, the Chao1 index, Observed species index, Shannon index, and Simpson index of the bacterial community in the sampling sites in the transition zone were higher than those in the sampling sites in the inflow area and the main reservoir area, indicating that the richness and diversity of the bacterial community in the sampling sites in the transition zone were the highest. The aerobic denitrifying bacteria in the sediments of Gangnan Reservoir mainly belong to Protebacteria. The first dominant class was β-Proteobacteria, and the first dominant genus was Thauera. A Venn diagram analysis indicated that the community of aerobic denitrification bacteria exhibited significant spatial and temporal differences. At the spatial level, there were higher numbers of different species based on LEfSe analysis than that at the seasonal level. Among the marker species screened by random forest analysis, Comamonas had the highest contribution in all spatial sampling sites, whereas Pectobacterium had the highest contribution in all seasonal sampling sites. Network analysis showed that there were nine modules, including 565 edges of 297 nodes; 47 keystone species were obtained based on the indicator OTUs analysis and network analysis. The principal co-ordinates analysis revealed that keystone species in the spatial distribution exhibited significant differences (Adonis, P<0.001). The results of this study provide scientific basis for the separation and identification of efficient aerobic denitrifying bacteria.

Rhizosphere impacts bacterial community structure in the tea (Camellia sinensis (L.) O. Kuntze.) estates of Darjeeling, India.

India contributes 28% of the world's tea production, and the Darjeeling tea of India is a world-famous tea variety known for its unique quality, flavour and aroma. This study analyzed the spatial distribution of bacterial communities in the tea rhizosphere of six different tea estates at different altitudes. The organic carbon, total nitrogen and available phosphate were higher in the rhizosphere soils than the bulk soils, irrespective of the sites. Alpha and beta diversities were significantly (p < 0.05) higher in the bulk soil than in the rhizosphere. Among the identified phyla, the predominant ones were Proteobacteria, Actinobacteria and Acidobacteria. At the genus level, only four out of 23 predominant genera (>1% relative abundance) could be classified, viz., Candidatus Solibacter (5.36 ± 0.36%), Rhodoplanes (4.87 ± 0.3%), Candidatus Koribacter (2.3 ± 0.67%), Prevotella (1.49 ± 0.26%). The rhizosphere effect was prominent from the significant depletion of more ASVs (n = 39) compared to enrichment (n = 11). The functional genes also exhibit a similar trend with the enrichment of N2 fixation genes, disease suppression and Acetoin synthesis. Our study reports that the rhizobiome of tea is highly selective by reducing the alpha and beta diversity while enriching the significant functional genes.