Variation In Bacterial Community Structure Research Articles

Plant-specific microbial diversity facilitates functional redundancy at the soil-root interface

Abstract Aims Plant-specific microbial diversity reflecting host-microbe coevolution was frequently shown at the structural level but less on the functional scale. We studied the microbiome of three compartments at the soil root interface (root endosphere, rhizosphere, bulk soil) of medicinal plants cultivated under organic management in Egypt. The study aimed to examine the impact of the rhizosphere on microbial community composition and diversity in desert agricultural soil, as well as to identify specific functions associated with the rhizosphere. Methods The microbiome community structure, diversity, and microbial functioning were evaluated through the utilization of 16S rRNA gene amplicon and shotgun metagenome sequencing. Results We found the typical rhizosphere effect and plant-species-specific enrichment of bacterial diversity. The annual plants Calendula officinalis and Matricaria chamomilla (Asteraceae) were more similar than the perennial Solanum distichum (Solanaceae). Altogether, plant species explained 50.5% of the variation in bacterial community structures in the rhizosphere. Our results indicate a stronger effect of the plant species in terms of modulating bacterial community structures in the rhizosphere than in root endosphere samples. The plant-driven rhizosphere effect could be linked to redundant plant beneficial functions in the microbiome, while enrichment of specific genes related to amino acid ion transport and metabolism, carbohydrate transport and metabolism, defense mechanisms, and secondary metabolites biosynthesis were more specific. Conclusions The study explores the microbiome continuum at the soil-root interface of medicinal plant species, revealing significant bacterial community structure shifts and plant specificity. The study provides insights into the essential microbiome components contributing to rhizosphere functionality.

Seasonal dynamics shaping bacterial community structure and networks in a Multi Geomorphological Unit System (MGUS) within the eastern Ulansuhai Lake Basin, North China

Different geomorphological units such as mountains, forests, fields, grasslands, sands and water, despite their distinct morphologies, are interconnected through micro-ecosystems that collectively maintain the balance of regional ecology. However, there is a lack of research concerning the spatial correlation among different landscape micro-ecosystems within a catchment area, hindering a comprehensive understanding of watershed systematic evolution across various landscape micro-ecosystems. To address this gap, seasonal variations in bacterial community structure and ecological network connectivity were investigated across different geomorphological units in the eastern Ulansuhai Lake Basin, North China. Water and soil samples were collected in May (beginning of the growing season, 23 samples) and November (end of the growing season, 20 samples) 2021. The diversity of bacterial communities within the Multi Geomorphological Unit System (MGUS) comprising “mountain, forest, field, grassland, sand and water” increased from May to November due to precipitation and human cultivation influences. Environmental characteristics, such as water and soil variations, exert a greater influence on bacterial community structure than differences in landscape units. The stability of the macro-ecological network structure within the MGUS was relatively high, with “water” playing a pivotal role in connectivity (the average betweenness centrality value of “water” was more than twice that of the other landscape samples). This led to the gradual emergence of deterministic processes in the construction of the bacterial community, shifting from stochastic processes (90.8 % drift effect in May) to biotic interactions (29.2 % heterogeneous selection in November). Furthermore, the bacterial community structure exhibited “macroscopic stability, with ‘water’ assuming a central role, while also showing microscopic variations, reflecting fluctuations in the contribution of dominant bacterial genera to the network structure over time”. Our study offers a core information analysis aimed at characterizing the temporal and spatial evolution of microbial community structure within an MGUS, thereby addressing a gap in microbial macroecology.

Different Adaption Strategies of Abundant and Rare Microbial Communities in Sediment and Water of East Dongting Lake.

The dynamics of aquatic microbes is of great importance for comprehending the acclimatisation and evolution of microorganisms in lake ecology. However, little is known about the adaption strategies of microbial communities in East Dongting Lake, which had special and complexity geographical characteristics. A semi-enclosed lake area (A) and a waterway connected to Yangtze River (B) both existed in the lake zone. Here, we investigated bacterial and fungal community diversity, community network and community assembly processes in sediment and water. The results indicated that the proportion of OTU numbers and their relative abundance for rare and abundant taxa were different obviously between sediment and water, but not between bacteria and fungi. However, abundant subcommunities dominated the shifts of bacterial community diversity and structure in A region, while rare subcommunities for fungal community diversity. Compared to fungal community, bacterial network was more compact and more key stones were identified as rare taxa. In addition, stochastic processes (dispersal limitation) drove the community assembly of abundant and rare subcommunities, but the effects of deterministic processes (including variable and heterogeneous selections) affected more on rare rather than abundant taxa. Partial Mantel test further indicated that the effect of environmental factors was a stronger force in shaping abundant bacterial subcommunities (TOC, NH4+-N, TN, and ORP) and rare fungal subcommunities (ORP). Environmental factors explained more of the variation in bacterial community structure than that in fungal community structure, although they had additional effects on fungal community diversity and community assembly. Moreover, bacterial community affected the fungal community as a biotic factor in water. This research provided new insights into better understanding of microbial communities in the complex environment of the East Dongting Lake.

Microbial biomarkers as indicators of sperm viability in an insect.

Our understanding of microbial variation in male reproductive tissues is poorly understood, both regarding how it varies spatially across different tissues and its ability to affect male sperm and semen quality. To redress this gap, we explored the relationship between male sperm viability and male gut and reproductive tract microbiomes in the Pacific field cricket, Teleogryllus oceanicus. We selected cohorts of males within our populations with the highest and lowest natural sperm viability and characterized the bacterial microbiota present in the gut, testes, seminal vesicle, accessory glands and the spermatophore (ejaculate) using 16S ribosomal RNA gene metabarcoding. We identified bacterial taxa corresponding to sperm viability, highlighting for the first time an association between the host's microbial communities and male competitive fertilization success. We also found significant spatial variation in bacterial community structure of reproductive tissue types. Our data demonstrate the importance of considering the microbial diversity of both the host gut and reproductive tract when investigating male fertility in wildlife and potentially human clinical settings.

Effects of Rehydration on Bacterial Diversity in the Rhizosphere of Broomcorn Millet (Panicum miliaceum L.) after Drought Stress at the Flowering Stage.

This study aimed to elucidate responses of the bacterial structure and diversity of the rhizosphere in flowering broomcorn millet after rehydration following drought stress. In this study, the broomcorn millet varieties 'Hequ red millet' (A1) and 'Yanshu No.10' (A2), known for their different drought tolerance levels, were selected as experimental materials. The plants were subjected to rehydration after drought stress at the flowering stage, while normal watering (A1CK and A2CK) served as the control. Soil samples were collected at 10 days (A11, A21, A1CK1, and A2CK1) and 20 days (A12, A22, A1CK2, and A2CK2) after rehydration. High-throughput sequencing technology was employed to investigate the variations in bacterial community structure, diversity, and metabolic functions in the rhizosphere of the broomcorn millet at different time points following rehydration. The findings indicated that the operational taxonomic units (OTUs) of bacteria in the rhizosphere of broomcorn millet were notably influenced by the duration of treatment, with a significant decrease in OTUs observed after 20 days of rehydration. However, bacterial Alpha diversity was not significantly impacted by rehydration following drought stress. The bacterial community in the rhizosphere of broomcorn millet was mainly composed of Actinobacteria and Proteobacteria. After rewatering for 10 to 20 days after drought stress, the abundance of Sphingomonas and Aeromicrobium in the rhizosphere soil of the two varieties of broomcorn millet decreased gradually. Compared with Yanshu No.10, the abundance of Pseudarthrobacter in the rhizosphere of Hequ red millet gradually increased. A Beta diversity analysis revealed variations in the dissimilarities of the bacterial community which corresponded to different rehydration durations. The relative abundance of bacterial metabolic functions in the rhizosphere of broomcorn millet was lower after 20 days of rehydration, compared to measurements after 10 days of rehydration. This observation might be attributed to the exchange of materials between broomcorn millet and microorganisms during the initial rehydration stage to repair the effects of drought, as well as to the enrichment of numerous microorganisms to sustain the stability of the community structure. This study helps to comprehend the alterations to the bacterial structure and diversity in the rhizosphere of broomcorn millet following drought stress and rehydration. It sheds light on the growth status of broomcorn millet and its rhizosphere microorganisms under real environmental influences, thereby enhancing research on the drought tolerance mechanisms of broomcorn millet.

Assembly processes and co-occurrence of bacterial communities in tree rhizosphere under Pb-Zn contamination

Rhizosphere bacteria are critical for supporting plant performance in stressful environments. Understanding the assembly and co-occurrence of rhizosphere bacterial communities contributes significantly to both plant growth and heavy metal accumulation. In this study, Ligustrum lucidum and Melia azedarach were planted in soils with simulated varying levels of Pb-Zn contamination. The Rhizosphere bacterial communities were investigated by using 16S rRNA gene sequencing. The impacts of Pb-Zn contamination on the diversity and structure of the rhizosphere bacterial community were found to be greater than those of both tree species. The variation in bacterial community structure in both trees was mainly driven by the combinations of Pb-Zn and soil properties. Deterministic processes (non-planted, 82 %; L. lucidum, 73 %; M. azedarach, 55 %) proved to be the most important assembly processes for soil bacterial communities, but both trees increased the importance of stochastic processes (18 %, 27 %, 45 %). The rhizosphere co-occurrence networks exhibited greater stability compared to the non-planted soil networks. Rare taxa played a dominant role in maintaining the stability of rhizosphere networks, as most of the keystone taxa within rhizosphere networks belonged to rare taxa. Dissimilarities in the structure and network complexity of rhizosphere bacterial communities were significantly associated with differences in tree biomass and metal accumulation. These variations in response varied between both trees, with L. lucidum exhibiting greater potential for phytoremediation in its rhizosphere compared to M. azedarach. Our results offer valuable insights for designing effective microbe-assisted phytoremediation systems.

Investigation of Variation in Bacterial Community Structure in Endangered Korean Fir Tree by Habitats

The Korean fir tree (Abies koreana), an endemic species of South Korea, is experiencing a severe decline in population due to climate change. Studies on the conservation of Korean fir have been extensive, yet research regarding its correlation with rhizosphere bacterial communities remains scarce, warranting further investigation. In this study, metagenome amplicon sequencing targeting the 16S rRNA V4 region was conducted to examine the presence of specific bacterial communities in Korean fir and to investigate potential differences based on habitat types (rhizosphere of native or cultivated trees, soil of dead trees, and bulk soil) and seasonal variations (April, June, September, November). Here we show that although we could not identify specific taxa highly specifically with Korean fir, the rhizosphere bacterial community in native trees exhibited less variability in response to seasonal changes compared to that in bulk soils. Suggesting the establishment of relatively stable bacterial populations around the Korean fir natural habitat. Further research on other types of rhizosphere and/or microbes is necessary to investigate the distinct relationship of Korean fir with microbial communities.

Bacterial community assembly driven by temporal succession rather than spatial heterogeneity in Lake Bosten: a large lake suffering from eutrophication and salinization.

Oligosaline lakes in arid and semi-arid regions play a crucial role in providing essential water resources for local populations. However, limited research exists on the impact of the environment on bacterial community structure in these lakes, co-occurrence patterns and the mechanisms governing bacterial community assembly. This study aims to address this knowledge gap by examining samples collected from five areas of Lake Bosten over four seasons. Using the 16S rRNA gene sequencing method, we identified a total of 510 to 1,005 operational taxonomic units (OTUs) belonging to 37 phyla and 359 genera in Lake Bosten. The major bacterial phyla were Proteobacteria (46.5%), Actinobacteria (25.9%), Bacteroidetes (13.2%), and Cyanobacteria (5.7%), while the major genera were hgcI_clade (12.9%), Limnohabitans (6.2%), and Polynucleobacter (4.7%). Water temperature emerged as the primary driver of these community structure variations on global level. However, when considering only seasonal variations, pH and nitrate were identified as key factors influencing bacterial community structures. Summer differed from other seasons in aspects of seasonal symbiotic patterns of bacterial communities, community assembly and function are different from other seasons. There were notable variations in bacterial community structures between winter and summer. Deterministic processes dominated community assembly, but there was an increase in the proportion of stochastic processes during summer. In summer, the functions related to photosynthesis, nitrogen fixation, and decomposition of organic matter showed higher abundance. Our findings shed light on the response of bacterial communities to environmental changes and the underlying mechanisms of community assembly in oligosaline lakes in arid regions.

Variations in bacterial diversity and community structure in the sediments of an alkaline lake in Inner Mongolia plateau, China.

Alkaline lakes are a special aquatic ecosystem that act as important water and alkali resource in the arid-semiarid regions. The primary aim of the study is to explore how environmental factors affect community diversity and structure, and to find whether there are key microbes that can indicate changes in environmental factors in alkaline lakes. Therefore, four sediment samples (S1, S2, S3, and S4) were collected from Hamatai Lake which is an important alkali resource in Ordos' desert plateau of Inner Mongolia. Samples were collected along the salinity and alkalinity gradients and bacterial community compositions were investigated by Illumina Miseq sequencing. The results revealed that the diversity and richness of bacterial community decreased with increasing alkalinity (pH) and salinity, and bacterial community structure was obviously different for the relatively light alkaline and hyposaline samples (LAHO; pH < 8.5; salinity < 20‰) and high alkaline and hypersaline samples (HAHR; pH > 8.5; salinity > 20‰). Firmicutes, Proteobacteria and Bacteriodetes were observed to be the dominant phyla. Furthermore, Acidobacteria, Actinobacteria, and low salt-tolerant alkaliphilic nitrifying taxa were mainly distributed in S1 with LAHO characteristic. Firmicutes, Clostridia, Gammaproteobacteria, salt-tolerant alkaliphilic denitrifying taxa, haloalkaliphilic sulfur cycling taxa were mainly distributed in S2, S3 and S4, and were well adapted to haloalkaline conditions. Correlation analysis revealed that the community diversity (operational taxonomic unit numbers and/or Shannon index) and richness (Chao1) were significantly positively correlated with ammonium nitrogen (r = 0.654, p < 0.05; r = 0.680, p < 0.05) and negatively correlated with pH (r = -0.924, p < 0.01; r = -0.800, p < 0.01; r = -0.933, p < 0.01) and salinity (r = -0.615, p < 0.05; r = -0.647, p < 0.05). A redundancy analysis and variation partitioning analysis revealed that pH (explanation degrees of 53.5%, pseudo-F = 11.5, p < 0.01), TOC/TN (24.8%, pseudo-F = 10.3, p < 0.05) and salinity (9.2%, pseudo-F = 9.5, p < 0.05) were the most significant factors that caused the variations in bacterial community structure. The results suggested that alkalinity, nutrient salt and salinity jointly affect bacterial diversity and community structure, in which one taxon (Acidobacteria), six taxa (Cyanobacteria, Nitrosomonadaceae, Nitrospira, Bacillus, Lactococcus and Halomonas) and five taxa (Desulfonatronobacter, Dethiobacter, Desulfurivibrio, Thioalkalivibrio and Halorhodospira) are related to carbon, nitrogen and sulfur cycles, respectively. Classes Clostridia and Gammaproteobacteria might indicate changes of saline-alkali conditions in the sediments of alkaline lakes in desert plateau.

Spatio-temporal variation of bacterial community structure in two intertidal sediment types of Jiaozhou Bay

The intertidal sediment environment is dynamic and the biofilm bacterial community within it must constantly adapt, but an understanding of the differences in the biofilm bacterial community within sediments of different types is still relatively limited. The semi-enclosed Jiaozhou Bay has a temperate monsoon climate, with strong currents at the mouth of the bay. In this study, the structure of the bacterial community in Jiaozhou Bay sediment biofilms are described using high-throughput 16 S rRNA gene sequencing and the effects of temporal change and different sediment environment types are discussed. Alpha diversity was significantly higher in sandy samples than in muddy samples. Sandy sediments with increased heterogeneity promote bacterial aggregation. Beta diversity analysis showed significant differences between sediment types and between stations. Proteobacteria and Acidobacteria were significantly more abundant at ZQ, while Campilobacterota was significantly more abundant at LC. The relative abundances of Bacteroidetes, Campilobacterota, Firmicutes, and Chloroflexi were significantly higher in the muddy samples, while Actinobacteria and Proteobacteria were higher in the sandy samples. There were different phylum-level biomarkers between sediment types at different stations. There were also different patterns of functional enrichment in biogeochemical cycles between sediment types and stations with the former having more gene families that differed significantly, highlighting their greater role in determining bacterial function. Bacterial amplicon sequence variant variation between months was less than KEGG ortholog variation between months, presumably the temporal change had an impact on shaping the intertidal sediment bacterial community, although this was less clear at the gene family level. Random forest prediction yielded a combination of 43 family-level features that responded well to temporal change, reflecting the influence of temporal change on sediment biofilm bacteria.

Insights on the assembly processes and drivers of soil microbial communities in different depth layers in an abandoned polymetallic mining district

Soil microbes, which play crucial roles in maintaining soil functions and restoring degraded lands, are impacted by heavy metal pollution. This study investigated the vertical distribution of bacterial communities along the soil profiles across four types of areas (heavy metal pollution level: tailings heap area > phytoremediation area > natural restoration area > original forest area) in an abandoned polymetallic mining district by 16S rRNA sequencing, and aimed to disentangle the assembly mechanisms and key drivers of the vertical variation in bacterial community structure. Bacterial diversity and composition were found to vary remarkably between the depth layers in all types of areas, with heterogeneous selection dominated the vertical distribution pattern of soil bacterial communities. Pearson correlation analysis and partial Mantel test revealed that soil nutrients mainly shaped the vertical distribution of bacterial microbiota along soil profiles in the original forest and natural restoration areas. Ni, As, and bioavailable As were the key drivers regulating the vertical variation of bacterial assemblages in the phytoremediation area, whereas Pb, pH, soil organic carbon, and available nitrogen were crucial drivers in the tailings heap area. These findings reveal the predominant assembly mechanisms and drivers governing the vertical distribution of soil bacterial microbiota and indicate the efficiency of phytoremediation and ecological restoration on ameliorating edaphic micro-ecosystems in heavy metal-contaminated areas.

Seasonal and Spatial Variations of Bacterial Community Structure in the Bailang River Estuary

Planktonic cells are a vital part of biogeochemical nutrient cycling and play an extremely important role in maintaining the balance of water ecosystems. In this study, surface water samples were collected in three seasons (spring, summer, and winter) 10 km along the estuary of the Bailang River to assess the relationship between environmental factors and the bacterial community structure, which was determined by high-throughput sequencing. The physicochemical properties of the samples, including the pH, salinity, and inorganic nitrogen (NH4+, NO3−, and NO2−), exhibited significant seasonal variations, and the diversity and structure of the bacterial community also varied seasonally. A redundancy analysis showed that the inorganic nitrogen (NH4+, NO3−, NO2−), pH, and salinity are key factors in shaping the bacterial community composition. Among the different seasons, the core taxa of bacterial communities were the same, and Actinobacteria, Cyanobacteria, and Proteobacteria were the key components during the three seasons. The bacterial diversity and structure also varied seasonally, but there were no significant differences in spatial composition. Based on a phylogenetic investigation of communities by reconstruction of unobserved states analysis, nitrogen-cycle-related processes include four dominant processes: nitrogen mineralization, nitrogen fixation, dissimilatory nitrate reduction, and denitrification. These results suggest that the bacterial community structure in the waters of the Bailang River estuary is subject to seasonal rather than spatial variation. These findings provide new evidence for studies of the seasonal variation of bacterial communities in estuaries.

The dependent correlation between soil multifunctionality and bacterial community across different farmland soils.

Microorganisms play a critical role in soil biogeochemical cycles, but it is still debated whether they influence soil biogeochemical processes through community composition and diversity or not. This study aims to investigate variation in bacterial community structure across different soils and its correlation to soil multifunctionality. Soil samples were collected from five typical farmland zones along distinct climatic gradients in China. The high-throughput sequencing (Illumina MiSeq) of 16S rRNA genes was employed to analyze bacterial community composition in each soil sample. Multivariate analysis was used to determine the difference in soil properties, microbial community and functioning, and their interactions. Cluster and discrimination analysis indicated that bacterial community composition was similar in five tested soil samples, but bacterial richness combined with soil enzyme activities and potential nitrification rate (PNR) contributed most to the differentiations of soil samples. Mantel test analysis revealed that bacterial community composition and richness were more significantly shaped by soil nutrient conditions and edaphic variables than bacterial diversity. As for soil multifunctionality, soil microbial community level physiological profiles were little affected by abiotic and biotic factors, while soil enzymes and PNR were also significantly related to bacterial community composition and richness, in addition to soil N and P availability. Cumulatively, soil enzymes' activities and PNR were greatly dependent on bacterial community composition and richness not diversity, which in turn were greatly modified by soil N and P availability. Therefore, in the future it should be considered for the role of fertilization in the modification of bacterial community and the consequent control of nutrient cycling in soil.

Seasonal Variation and Influencing Factors of Bacterial Communities in Storage Reservoirs

In order to explore the seasonal variation and influencing factors of bacterial community structure in storage reservoirs, the impact of environmental factors must first be examined. In this study, the seasonal variation in bacterial community structure and its response to water quality factors were explored by monitoring the water quality of Qingdao Jihongtan Reservoir, the only reservoir of the Yellow River diversion project, using high-throughput sequencing technology and symbiotic network analysis. The results showed that the diversity and richness of bacterial communities were highest in summer and lowest in winter, and those in the inlet were higher than those in the outlet. The structure of the bacterial community was similar in spring and winter and in summer to autumn. The dominant bacteria phyla were:Actinobacteriota (6.63%-57.38%), Proteobacteria (11.32%-48.60%), Bacteroidota (5.05%-25.74%), and Cyanobacteria (0.65%-24.74%). Additionally, the abundances of Chloroflexi, Dependentiae, Fusobacteriota, and Margulisbacteria were the highest in autumn and the lowest in winter. The dominant bacterial genera were:hgcI_clade (3.72%-34.66%), CL500_29_marine_group (0.31%-20.13%), and Limnohabitans (0.16%-10.37%). Further, the abundances of Flavobacterium, Polaromonas, and Rhodoferax were the highest in winter and the lowest in summer; the trend of Domibacillus and Limnobacter was the opposite. The abundance of Proteobacteria and Campilobacteria in the inlet was significantly higher than that in the outlet, and the Planctomycetota showed the opposite. The abundances of Dinghuibacter, Arenimonas, and Rhodobacter in the inlet were significantly higher than those in the outlet. Competition and antagonism dominated the interaction relationship of bacterial communities in spring, whereas mutualism dominated in winter. There were significant differences among key species in the symbiotic network at different seasons and sampling sites. Water temperature, DO, water storage capacity, and water storage sources had a great influence on bacterial community structure in the Jihongtan Reservoir.

Combined impacts of algae-induced variations in water soluble organic matter and heavy metals on bacterial community structure in sediment from Chaohu Lake, a eutrophic shallow lake

Many lakes are suffering from eutrophication and heavy metals-contamination. However, the combined impacts of algae bloom and its induced variations in heavy metals on microbial community in sediment from eutrophic lakes remain unclear. In this study, we performed field experiments to investigate how algae bloom impacted water soluble organic matter (WSOM) and heavy metals in sediment from Chaohu Lake, a eutrophic shallow lake, and probed their combined impacts on sediment bacterial community structure. The results showed that algae bloom increased WSOM quantity, in particular, the soluble microbial by-product-like (SMP) and fulvic acid-like (Fa-L) components markedly enhanced by 203.70 % and 70.17 %, respectively. We also found that algae bloom redistributed the spatial patterns of heavy metals and altered their chemical species in sediment, then promoted contamination degree and potential ecological risk of heavy metals in sediment. Moreover, sediment bacterial community richness and diversity obviously decreased after algae bloom, and the variance partitioning analysis (VPA) results showed that combined impacts of algae-induced changes in WSOM and heavy metals explained 66.56 % of the variations in bacterial community structure. These findings depicted how algae bloom influence sediment WSOM and heavy metals, and revealed the combined impacts of algae-induced variations on microbial community structure in shallow eutrophic lake.

Quantifying relative contributions of biotic interactions to bacterial diversity and community assembly by using community characteristics of microbial eukaryotes

Biotic interactions are known as a major control on microbial diversity. However, biotic interactions have rarely been quantified in an adequate manner, often leaving much residual variation unexplained in microbial biogeographic studies. Herein, we propose a holistic approach to disentangle the relative importance of inter-domain interactions in shaping microbial diversity by incorporating community-level characteristics. Taking coastal bacterioplankton on a regional scale as an example, we designated a range of community characteristics of pico- and nanoeukaryotes derived from metabarcoding and flow cytometric data as inter-domain interacting proxies, which were then considered in statistical modeling. We found that the bacterial diversity indices and community structure were much more accurately explained by a number of eukaryotic characteristics than by the measured environmental variables and/or spatial variables alone, as were the richness, relative abundances, and assemblage structures of major bacterial taxa. In co-occurrence networks, the nodes of characteristics that had more edges (links) were frequently the best explanatory variables for bacterial diversity indices. Over 70% of total variation in bacterial community structure could be explained by three categories of biotic interactions: parasitism (27%), fungi-bacterial competition (32%), and trophic structure and bacterivory (13%). This study showcases a methodological framework to infer different types of inter-domain interactions at play, and stresses the importance of non-grazing interacting processes in shaping bacterial diversity and community assembly.

Patterns of groundwater bacterial communities along the petroleum hydrocarbon gradient

Groundwater contamination by petroleum hydrocarbons has become a worldwide environmental problem. Despite that microorganisms played an important role in biogeochemical processes such as hydrocarbon degradation, comprehensive understanding of the structure, function, and interactions of groundwater bacterial communities in petroleum hydrocarbon-contaminated sites is still lacking. Here we investigated the groundwater bacterial communities along a total petroleum hydrocarbon gradient (TPH: 0.01–2.09 mg/L) at an abandoned chemical factory site by sequencing microbial 16 S rRNA gene amplicons. Results showed that hydrocarbon contamination in groundwater reduced the bacterial diversity, and favored the growth of some species, such as members of the β-, γ-Proteobacteria and Planctomycetes. TPH exerted profound selection pressure on the bacterial community, as the variation of community structure along the TPH gradient were significantly correlated with the petroleum hydrocarbon tolerance of the community (r = 0.362; p < 0.001). Other geochemical variables of the groundwater, including pH, sampling depth, oxidation-reduction potential, temperature, and dissolved oxygen, also influenced the community structure. Variations in bacterial community structure thus altered the functional potential, with significantly higher alkane (alkB and alkH) and PAH (nahF and phdK) degradation gene abundances in the relatively high contaminated sampling wells. By conducting the ecological network analysis, we identified a potentially important ecological module relating to petroleum hydrocarbon degradation, which is mainly composed of members of Proteobacteria. This suggested the potential metabolic cross-feeding relationship of Proteobacteria in utilizing petroleum hydrocarbon. These findings illustrate an overall picture of bacterial communities involved in a petroleum hydrocarbon contamination site and provided useful information for groundwater restoration and environmental management.

Ratio of carbon and nitrogen in fertilizer treatment drives distinct rhizosphere microbial community composition and co-occurrence networks.

Fertilization is the main strategy to accelerate vegetation restoration and improve the rhizosphere microbial community in the northeast China. However, the responses of rhizosphere microbial community structure, specific microbial community and symbiotic pattern to manure fertilization in grassland (alfalfa only) are not well clear. In this study, the variation of bacterial community structures in R_Manure (extracted liquid of fermented cow manure), E_Manure (extracted residue of fermented cow manure), F_Manure (full fermented cow manure), and Control (without fermented cow manure) collected from the rhizosphere microbial community of alfalfa were analyzed by the application of an Illumina HiSeq high-throughput sequencing technique. A total of 62,862 microbial operational taxonomic units (OTUs) were detected and derived from 21 phyla of known bacteria. The dominant bacteria in the rhizosphere include Proteobacteria (70.20%), Acidobacteria (1.24%), Actinobacteria (2.11%), Bacteroidetes (6.15%), Firmicutes (4.21%), and Chlorofexi (2.13%) accounting for 86% of the dominant phyla in all treatments. At the genus level, the dominant genus include NB1-j, Lysobacter, Alphaproteobacteria, Subgroup_6, Actinomarinales, Saccharimonadales, Aneurinibacillus, MO-CFX2, SBR1031, Caldilineaceae, and so on with the average relative abundance (RA) of 1.76%, 1.52%, 1.30%, 1.24%, 1.61%, 2.39%, 1.36%, 1.42%, 1.27%, and 1.03%, respectively. Bacterial diversities and community structures were significantly differentiated by different treatments of fertilization. The results of community structure composition showed that R_Manure treatment significantly increased the population abundance of Firmicutes, Chlorofexi, and Patescibacteria by 34.32%, 6.85%, and 2.70%, and decreased the population abundance of Proteobacteria and Actinobacteria by 16.83% and 1.04%, respectively. In addition, it showed that all treatments significantly resulted in an increase or decrease at the genus level. R_Manure had the higher richness and diversity of the bacterial community, with the greatest topology attributes of the co-occurrence networks. Through the analysis of the molecular ecological network (MENA), the co-occurrence networks had a shorter average path distance and diameter in R_Manure than in others, implying more stability to environmental changes. Redundancy analysis (RDA) showed that the ratio of carbon and nitrogen (C/N) was the main factor affecting rhizosphere microbial community composition while driving distinct rhizosphere bacterial community and its co-occurrence networks. The R_Manure associated with more C/N had relatively complex microbial co-occurrence network with a large number of nodes and edges, while the microbial network of others associated with less C/N had fewer taxa with loose mutual interactions. These results suggested that organic fertilizer with high C/N can regulate the rhizosphere microorganism, while high C/N can determine bacterial community structures, specific bacterial taxa, and their relationships with the nodule size of alfalfa. These significant changes can be used to evaluate soil fertility and fertilizer management in the artificial grassland system, while the potential biological indicators of the rhizosphere microbial community will play an important role in future eco-agriculture.

Stagnation trigger changes to tap water quality in winter season: Novel insights into bacterial community activity and composition

The drinking water distribution system is important for water supply and it affects the quality of the drinking water. Indoor pipeline water quality is regulated by physical, hydraulic and biological elements, such as indoor temperature and stagnation. In this work, the effects of indoor heating and overnight stagnation on the variation in bacterial community structure and the total cell count were assessed by full-length 16S rRNA gene sequencing and flow cytometry, respectively. The results exhibited that the average intact cell count was 6.99 × 104 cells/mL and the low nucleic acid (LNA) bacteria was 4.48 × 104 cells/mL after stagnation. The average concentration of total and intracellular adenosine triphosphate (ATP) was 3.64 × 10−12 gATP/mL and 3.13 × 10−17 gATP/cell in stagnant water, respectively. The growth of LNA cells played a crucial role in increasing ATP. The dominant phylum observed was Proteobacteria (87.21 %), followed by Actinobacteria (8.25 %). Opportunistic pathogens increased the risk of disease in stagnant water (up to 1.2-fold for Pseudomonas sp. and 5.8-fold for Mycobacterium sp.). Meanwhile, structural equation model (SEM) and redundancy analysis (RDA) also illustrated that water temperature, residual chlorine and Fe significantly affected the abundance and composition of bacterial community. Taking together, these results show response of tap water quality to overnight stagnation and indoor heating, and provide scientific basis for drinking water security management in winter season.

Effects of Environmental Factors on the Spatial Succession of the Bacterial Community in Municipal Solid-Waste Landfills

Secondary pollution control and rapid stabilization of municipal solid waste (MSW) landfills are closely associated with bacterial communities. The spatial variations in bacterial community structure and the environmental factors controlling it were studied by the 16S rRNA gene sequencing of MSW sampled at different depths in a large sanitary landfill (LSL) and a medium non-sanitary landfill (MNSL), respectively. The total nitrogen (TN) and total phosphorus (TP) content in the LSL and MNSL samples displayed a downward trend as the depth increased. However, the organic matter (OM) content followed the opposite trend. Diversity of microbes was highest in the middle layer of both the LSL and MNSL. Firmicutes and Proteobacteria were the dominant phylum both in the LSL and MNSL. In the LSL, the dominant bacteria genera succeeded from Psychrobacter, Pseudomonas to Clostridium, Savagea. However, in the MNSL, the genera succeeded from Uncultured, Pleomorphomonas to Hydrogenispora, Acetomicrobium. The type of landfill and the different environmental factors control the succession of the bacterial community in LSL and MNSL. The pH, OM, TN, and TP will change in the landfill as the landfill depth increased. The impact degree of landfill depth on pH, OM, TN, and TP content in the LSL was 15.3%, 16.1%, 4.9%, and 4.2%, respectively. These values were lower than those in the MNSL. In addition, depth and OM had the strongest correlations but no significance with the dominant bacteria both in the LSL (|Rdepth|average=0.48;|ROM|average=0.36) and MNSL (|Rdepth|average=0.51;|ROM|average=0.36). This indicated that bacterial community succession was mainly dependent on space, time, and MSW characteristics in different types of landfills.