Bacterial Functional Diversity Research Articles

Responses of soil bacterial functional group diversity to nitrogen enrichment in global grasslands

Soil microbial functional groups are closely linked to ecosystem functioning and are highly sensitive to global environmental changes. However, compared to the species diversity, how soil microbial functional group diversity responds to environmental changes remains poorly understood. Here, we investigated the nitrogen (N) effect on soil bacterial functional group diversity and predicted its spatial pattern in global grasslands. By re-analyzing publicly available 16S rRNA gene amplicon data from 38 N-addition experiments including 96 paired measurements across five continents, we found that N enrichment significantly leads to a more similar β-diversity but had no pronounced effect on α-diversity of soil bacterial functional groups. Global mapping with a random forest model revealed a clear spatial pattern of the N effect: ∼78 % of the global grasslands have shifted towards a more similar bacterial functional group β-diversity under contemporary N deposition rates, and in the regions particularly affected by high N deposition and vulnerable to global changes (e.g. the Eurasian steppe), the magnitude of change was greater. These results make a step in understanding soil microbial functional group diversity in addition to species diversity in the face of environmental changes, and provide more knowledge and rationale for the conservation of soil microbial functional diversity hotspots in global grasslands.

Climate and local environment co-mediate the taxonomic and functional diversity of bacteria and archaea in the Qinghai-Tibet Plateau rivers

Understanding the environmental response patterns of riverine microbiota is essential for predicting the potential impact of future environmental change on river ecosystems. Vulnerable plateau ecosystems are particularly sensitive to climate and local environmental changes, however, the environmental response patterns of the taxonomic and functional diversity of riverine microbiota remain unclear. Here, we conducted a systematic investigation of the taxonomic and functional diversity of bacteria and archaea from riparian soils, sediments, and water across the elevation of 1800– 4800 m in the Qinghai-Tibet Plateau rivers. We found that within the elevation range of 1800 to 3800 m, riparian soils and sediments exhibited similarities and stabilities in microbial taxonomic and functional diversity, and water microbiomes were more sensitive with great fluctuations in microbial diversity. Beyond the elevation of 3800 m, microbial diversity declined across all riverine matrixes. Local environmental conditions can influence the sensitivity of microbiomes to climate change. The combination of critical climate and local environmental factors, including total nitrogen, total organic carbon, as well as climate variables associated with temperature and precipitation, provided better explanations for microbial diversity than single-factor analyses. Under the extremely adverse scenario of high greenhouse gas emission concentrations (SSP585), we anticipate that by the end of this century, the bacterial, archaeal, and microbial functional diversity across the river network of the Yangtze and Yellow source basin would potentially change by −16.9– 5.2 %, −16.1– 5.7 %, and −9.3– 6.4 %, respectively. Overall, climate and local environments jointly shaped the microbial diversity in plateau river ecosystems, and water microbiomes would provide early signs of environmental changes. Our study provides effective theoretical foundations for the conservation of river biodiversity and functional stability under environmental changes.

Increased bacterial taxonomic and functional diversity is associated with impaired rotavirus vaccine immunogenicity in infants from India and Malawi

The immunogenicity and effectiveness of oral rotavirus vaccines (ORVs) against severe rotavirus-associated gastroenteritis are impaired in low- and middle-income countries (LMICs) where the burden of disease is highest. Determining risk factors for impaired ORV response may help identify strategies to enhance vaccine effectiveness. In this study, we use metagenomic sequencing to provide a high-resolution taxonomic analysis of stool samples collected at 6 weeks of age (coinciding with the first ORV dose) during a prospective study of ORV immunogenicity in India and Malawi. We then analyse the functional capacity of the developing microbiome in these cohorts. Microbiome composition differed significantly between countries, although functional capacity was more similar than taxonomic composition. Our results confirm previously reported findings that the developing microbiome is more diverse in taxonomic composition in ORV non-seroconverters compared with seroconverters, and we additionally demonstrate a similar pattern in functional capacity. Although taxonomic or functional feature abundances are poor predictors of ORV response, we show that skews in the direction of associations within these microbiome data can be used to identify consistent markers of ORV response across LMIC infant cohorts. We also highlight the systemic under-representation of reference genes from LMICs that limit functional annotation in our study (7% and 13% annotation at pathway and enzyme commission level, respectively). Overall, higher microbiome diversity in early life may act as marker for impaired ORV response in India and Malawi, whilst a holistic perspective of functional capacity may be hidden in the “dark matter” of the microbiome.

Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient

Bacterial gene repertoires reflect adaptive strategies, contribute to ecosystem functioning and are limited by genome size. However, gene functional diversity does not necessarily correlate with taxonomic diversity because average genome size may vary by community. Here, we analyse gene functional diversity (by shotgun metagenomics) and taxonomic diversity (by 16S rRNA gene amplicon sequencing) to investigate soil bacterial communities along a natural pH gradient in 12 tropical, subtropical, and temperate forests. We find that bacterial average genome size and gene functional diversity decrease, whereas taxonomic diversity increases, as soil pH rises from acid to neutral; as a result, bacterial taxonomic and functional diversity are negatively correlated. The gene repertoire of acid-adapted oligotrophs is enriched in functions of signal transduction, cell motility, secretion system, and degradation of complex compounds, while that of neutral pH-adapted copiotrophs is enriched in functions of energy metabolism and membrane transport. Our results indicate that a mismatch between taxonomic and functional diversity can arise when environmental factors (such as pH) select for adaptive strategies that affect genome size distributions.

Uncovering the Resistome of a Peruvian City through a Metagenomic Analysis of Sewage Samples

Background: Antibiotic resistance is a major public health concern globally. In this study, we aimed to evaluate the abundance and diversity of antibiotic resistance genes (ARGs) in sewage water samples from two hospitals and an adjacent community or urban setting in Huanuco, a Peruvian city located in the highlands. Methods: We collected samples from the community wastewater system and from sewage pipes from the two hospitals in Huanuco. DNA was extracted from 250 mL of sewage water samples (n = 6) and subjected to microbiome profiling using 16S rRNA short amplicon sequencing and shotgun metagenomics. We analyzed the taxonomic and functional content in all samples, including alpha and beta diversity metrics, and searched for ARGs. Results: Our results showed that samples taken from the community wastewater system were compositionally different and harbored greater bacterial taxonomic and functional diversity compared to samples collected from the hospitals’ wastewater system. We found a high abundance of bacteria associated with resistance to beta-lactams, macrolides, aminoglycosides, fluoroquinolones, and tetracyclines in all samples. However, there were no significant differences in the abundance or composition of ARGs between the community wastewater samples and those taken from the two hospitals. Conclusions: Our findings suggest that metagenomics analyses in wastewater sewage could be a useful tool for monitoring antibiotic resistance in urban settings. These data could be used to develop local public health policies, particularly in cities or countries with limited resources to establish large-scale One Health projects.

Biochar amendment alleviates heavy metal phytotoxicity of Medicago sativa grown in polymetallic contaminated soil: Evaluation of metal uptake, plant response and soil properties

Air pollution and soil contamination have caused major environmental damage in the industrial complex of Gabes. This study aimed to evaluate the abilities of biochar to modify soil properties and assess the adaptation of alfalfa (Medicago sativa L.) plants in contaminated soils from the Gabes Region. The experiment was executed with soil samples from three sites (S1, S2 and S3) located at different distances from the industrial zone of Gabes. Additionally, a control soil was included for comparison. Pot experiments were performed under controlled conditions, with or without biochar. After 60 days, the accumulation of heavy metals in plants (roots, shoots and nodules) was determined. Moreover, oxidative stress biomarkers, such as malondialdehyde (MDA) content, glutathione-S-transferase (GST) and catalase (CAT), were evaluated. Soil microbiological properties, including bacterial functional diversity and fluorescein diacetate hydrolytic (FDA) activity, were analyzed, along with soil chemical properties. Our results revealed that biochar supplementation can improve microbial functions and cation-exchange capacity (CEC), thereby increasing the availability of nutrients to plants. Interestingly, the application of biochar resulted in decreased concentrations of copper (Cu) and zinc (Zn) in plants, which may be attributed to a reduction in their bioavailability in the soil. The accumulation of heavy metals in alfalfa organs was positively correlated with the levels of MDA and antioxidant enzymes in both leaves and roots. In this study, the addition of biochar reduced the antioxidant mechanisms of alfalfa and mitigated the negative effects of metals, resulting in a positive impact on growth and chlorophyll content. Our data highlights the beneficial effects of biochar on enhancing crop productivity and remediating contaminated soil.

Endophytic bacterial taxonomic and functional diversity in the seeds of wheat genotypes from different agroecologies

ABSTRACT Plant genotype and agroecology influence the composition and functionality of seed endophytic bacterial communities. Taxonomic analysis of 123 wheat seeds endophytic bacteria classified these into 23 genera predominantly under Firmicutes followed by Actinobacteria and Proteobacteria. Genus Bacillus was most abundant (30.7%) followed by Streptomyces (18.4%) with other representative genera such as Stenotrophomonas, Paenibacillus, Mixta, Enterobacter, Micrococcus, Pantoea, Alkalihalobacillus, Cortiobacterium, and more. Across agroecologies, the core microbiota of seeds consists of Bacillus, Streptomyces, Paenibacillus, and Stenotrophomonas, with maximum diversity and abundance observed in seeds of the North Western Plain Zone of India. Seed endophytic bacteria had PGP traits; nitrogen fixation (n = 101), production of IAA (n = 65), siderophores (n = 43), ammonia (n = 82) and solubilization of phosphate (n = 47), potassium (n = 37), and zinc (n = 8). The isolates produced HCN and hydrolytic enzymes and displayed antagonism against fungal pathogens. Overall, the information generated on wheat seeds’ endophytic bacterial taxonomy and beneficial traits may pave the path for the development of novel bioinoculants. Key message Wheat seeds from various agro-ecologies of India harbor diverse endophytic bacteria. Firmicutes were dominant followed by Actinobacteria and Proteobacteria. Genus Bacillus, Stenotrophomonas, Streptomyces, and Paenibacillus were core endophytic bacteria in different agro-ecologies. The endophytic bacterial strains were displaying diverse functional traits.

Soil amendment and rhizobacterial inoculation improved Cu phytostabilization, plant growth and microbial activity in a bench-scale experiment.

Mine driven trace elements' pollution entails environmental risks and causes soil infertility. In the last decades, in situ techniques such as phytostabilization have become increasingly important as ways to tackle these negative impacts. The aim of this study was to test the individual and combined effects of different aided phytostabilization techniques using substrate from barren tailings of a Cu mine, characterized by extreme infertility (high acidity and deficiency of organic matter and nutrients). The experiment analyzed the growth of Populus nigra L. planted alone (P) or in co-cropping with Trifolium repens L. (PT), in pots containing mine soil amended with compost (1, 10, compost, soil, w/w) non inoculated (NI) or inoculated with plant growth promoting rhizobacteria (PGP), mycorrhizae (MYC) or a combination of bacterial and fungal inocula (PGPMYC). Non-amended, non-planted and non-inoculated reference ports were also prepared. Plants were harvested after 110 days of plant development and several biometric and phytopathological parameters (stem height, aerial biomass, root biomass, wilting, chlorosis, pest and death) and macro and micronutrient composition were determined. The growth substrate was analyzed for several physicochemical (pH, CECe, and exchangeable cations, total C and N, P Olsen and availability of trace elements) and microbiological (community level physiological profiles: activity, richness and diversity) parameters. The use of the amendment, P. nigra plantation, and inoculation with rhizobacteria were the best techniques to reduce toxicity and improve soil fertility, as well as to increase the plant survival and growth. Soil bacterial functional diversity was markedly influenced by the presence of plants and the inoculation with bacteria, which suggests that the presence of plant regulated the configuration of a microbial community in which the inoculated bacteria thrive comparatively better. The results of this study support the use of organic amendments, tolerant plants, and plant growth promoting rhizobacteria to reduce environmental risk and improve fertility of soils impacted by mining.

Eco-evolutionary implications of helminth microbiomes.

The evolution of helminth parasites has long been seen as an interplay between host resistance to infection and the parasite's capacity to bypass such resistance. However, there has recently been an increasing appreciation of the role of symbiotic microbes in the interaction of helminth parasites and their hosts. It is now clear that helminths have a different microbiome from the organisms they parasitize, and sometimes amid large variability, components of the microbiome are shared among different life stages or among populations of the parasite. Helminths have been shown to acquire microbes from their parent generations (vertical transmission) and from their surroundings (horizontal transmission). In this latter case, natural selection has been strongly linked to the fact that helminth-associated microbiota is not simply a random assemblage of the pool of microbes available from their organismal hosts or environments. Indeed, some helminth parasites and specific microbial taxa have evolved complex ecological relationships, ranging from obligate mutualism to reproductive manipulation of the helminth by associated microbes. However, our understanding is still very elementary regarding the net effect of all microbiome components in the eco-evolution of helminths and their interaction with hosts. In this non-exhaustible review, we focus on the bacterial microbiome associated with helminths (as opposed to the microbiome of their hosts) and highlight relevant concepts and key findings in bacterial transmission, ecological associations, and taxonomic and functional diversity of the bacteriome. We integrate the microbiome dimension in a discussion of the evolution of helminth parasites and identify fundamental knowledge gaps, finally suggesting research avenues for understanding the eco-evolutionary impacts of the microbiome in host-parasite interactions in light of new technological developments.

Diversity and activity of soil biota at a post-mining site highly contaminated with Zn and Cd are enhanced by metallicolous compared to non-metallicolous Arabidopsis halleri ecotypes.

Hyperaccumulators' ability to take up large quantities of harmful heavy metals from contaminated soils and store them in their foliage makes them promising organisms for bioremediation. Here we demonstrate that some ecotypes of the zinc hyperaccumulator Arabidopsis halleri are more suitable for bioremediation than others, because of their distinct influence on soil biota. In a field experiment, populations originating from metal-polluted and unpolluted soils were transplanted to a highly contaminated metalliferous site in Southern Poland. Effects of plant ecotypes on soil biota were assessed by measurements of feeding activity of soil fauna (bait-lamina test) and catabolic activity and functional diversity of soil bacteria underneath A. halleri plants (Biolog® ECO plates). Chemical soil properties, plant morphological parameters, and zinc concentration in shoots and roots were additionally evaluated. Higher soil fauna feeding activity and higher bacterial community functional diversity were found in soils affected by A. halleri plants originating from metallicolous compared to non-metallicolous ecotypes. Differences in community-level physiological profiles further evidenced changes in microbial communities in response to plant ecotype. These soil characteristics were positively correlated with plant size. No differences in zinc content in shoots and roots, zinc translocation ratio, and plant morphology were observed between metallicolous and non-metallicolous plants. Our results indicate strong associations between A. halleri ecotype and soil microbial community properties. In particular, the improvement of soil biological properties by metallicolous accessions should be further explored to optimize hyperaccumulator-based bioremediation technologies.

How Important Are the Relations between Vegetation Diversity and Bacterial Functional Diversity for the Functioning of Novel Ecosystems?

Understanding ecosystem development of post-mining areas requires observing the development of the plant and microbial communities. It is widely known that mutual interaction is important for both of these groups, and both benefit significantly. The aim of this study was to broaden the knowledge about the relation between the vegetation and functional diversity of bacterial communities in novel ecosystems of post-mining areas and to discuss the potential applicability of methods of studies of bacterial functional diversity in these ecosystems with special attention paid to the BIOLOG method. The functional diversity of microbial communities of five types of microhabitats of post-coal mining heap (Upper Silesia, Poland) was studied using the BIOLOG method. Four of them were covered by spontaneously developed vegetation (two dominated by grasses Calamagrostis epigejos and Poa compressa and two others by dicotyledonous species Daucus carota and Tussilago farfara). The results obtained for vegetated microhabitats were compared with the diversity of microbial communities from non-vegetated types of microhabitat. Our study confirmed that microbial functional diversity measured by the summed area under the curve for all substrates, the richness index, the Shannon-Wiener index and the evenness index mirrors aboveground vegetation diversity. All of these measures differ, especially between non-vegetated patches and grassland patches dominated by C. epigejos and P. compressa.

High Throughput Sequencing Reveals Distinct Bacterial Communities and Functional Diversity in Two Typical Coastal Bays

The marine waters in semi-enclosed bays are highly dynamic and strongly influenced by different levels of anthropogenic activity. This study explored the bacterial community composition and diversity in two typical urbanized coastal bay areas (Shenzhen Bay (S) and Dapeng Bay (D)) in Shenzhen, China, based on Illumina NovaSeq sequencing. Seawater analysis showed that coastal area S experienced a higher level of pollution, with higher nutrient concentrations observed. Alpha diversity analysis showed a higher bacterial diversity and richness in coastal area S than D. Taxonomic analysis revealed that the phylum Proteobacteria showed the highest abundance in all samples. Other dominant phyla were Firmicutes, Cyanobacteria, Tenericutes, and Actinobacteria. The bacterial community compositions were significantly different between the two coastal areas. A significant community difference was also found between the sampling sites of coastal area S. However, the difference between sampling sites in coastal area D was not significant. Physicochemical factors showed a more significant effect on bacterial community composition than nutrients. Pearson correlation tests and Network analysis further confirmed that salinity/conductivity, pH, and nitrate were the key factors driving the community difference. PICRUSt analysis revealed a higher degree of functional pathways in coastal area S relating to carbohydrate metabolism, membrane transport, and xenobiotics biodegradation. Our results provide in-depth insights into the bacterial community compositions in typical polluted coastal bays. They may provide information on underlying factors of the assembly process in microbial communities in the coastal zone.

Degradation-driven bacterial homogenization closely associated with the loss of soil multifunctionality in alpine meadows

Alpine meadows are sensitive to climate change due to their unique ecosystem. The mechanisms by which soil microbial diversity regulates soil multifunctionality under degradation need to be extensively explored. In this study, three degraded levels of alpine meadows (nondegraded, ND; moderately degraded, MD; and severely degraded, SD) were chosen in the hinterland of Sanjiangyuan National Park on the Qinghai–Tibet Plateau. Soil microbial abundance and community structure were determined through 16 S rRNA, and six soil variables related to nutrient pools (DNA concentration, CDNA; soil organic matter, SOM; total N, TN; total P, TP; hydrolytic N, HN; and available P, AP) were measured and calculated for soil multifunctionality. The results showed that meadow degradation resulted in a decline in bacterial functional diversity and an increase in compositional diversity (Shannon index and richness). Soil fungi were less sensitive to meadow degradation. Meanwhile, soil individual functions, such as SOM, TN, HN, AP, and multifunctionality, decreased significantly when subjected to meadow degradation. Moreover, bacterial functional diversity and the Shannon index, rather than bacterial richness, had significantly positive and negative relationships with soil multifunctionality, respectively. Furthermore, the dissimilarity of bacterial communities decreased with degradation. These results indicated that meadow degradation led to bacterial homogenization and functional redundancy, all of which would reduce soil multifunctionality. Abiotic factors such as soil water content (SWC) and bulk density (BD) also significantly changed and still played a key role in regulating the soil multifunctionality accompanying degradation. Amino-acid metabolism had the highest relative abundance (4.37%) and was negatively correlated with SOM and TN, implying that bacteria may convert more limited resources for their own needs and increase the loss of soil multifunctionality under severe degradation. The results provide new insight into the relationships between biodiversity and ecosystem multifunctionality and scientific guidance for the restoration of degraded alpine meadows.

Sorption–Desorption of Imazamox and 2,4-DB in Acidic Mediterranean Agricultural Soils and Herbicide Impact on Culturable Bacterial Populations and Functional Diversity

In this study, we investigated the sorption–desorption behavior of imazamox (IMZ) and 2,4-DB (DB) in two typical acidic Mediterranean agricultural soils and the impact of these herbicides on culturable soil bacterial populations, enzyme activities and functional diversity when applied at concentrations higher than recommended doses (10×, 50×, 500×). Herbicide sorption was similar in both soils and IMZ was less retained compared to DB (~0.5 vs. 40 µg g−1 soil, respectively). IMZ desorption was remarkable (70–100%) while that of DB was more limited, i.e., ~40%. Three days after spiking (DAS), IMZ and DB significantly increased the number of soil-culturable heterotrophic bacteria, actinomycetes and Pseudomonas spp., soil respiration and the potential catabolic capacity of soil microbial communities. Soil dehydrogenase activity increased by ~56–70% in IMZ-treated soils while being reduced by ~33–41% in DB-treated ones. β-glucosidase activity showed a soil-dependent behavior, while the pattern of C source utilization suggested a change of soil microbial community structure after herbicide (especially DB) spiking. At 30 DAS, the herbicides’ impact on soil microorganisms, enzyme activity and functional diversity was still visible. Moreover, a toxic effect of DB (at 50× and 500×), but not IMZ, was recorded vs. Rhizobium sullae, the bacterial symbiont of Hedysarum coronarium. The obtained results indicated that IMZ and DB are poorly sorbed and highly desorbed by both soils. Moreover, at the tested concentrations, IMZ and DB can have short- and medium-term impacts on the microbial component and the related activity of the investigated soils, likely affecting a range of ecosystem services provided by soil microorganisms.

Bacterial Communities in the Rhizosphere at Different Growth Stages of Maize Cultivated in Soil Under Conventional and Conservation Agricultural Practices.

ABSTRACTFarmers in Mexico till soil intensively, remove crop residues for fodder and grow maize often in monoculture. Conservation agriculture (CA), including minimal tillage, crop residue retention and crop diversification, is proposed as a more sustainable alternative. In this study, we determined the effect of agricultural practices and the developing maize rhizosphere on soil bacterial communities. Bulk and maize (Zea mays L.) rhizosphere soil under conventional practices (CP) and CA were sampled during the vegetative, flowering and grain filling stage, and 16S rRNA metabarcoding was used to assess bacterial diversity and community structure. The functional diversity was inferred from the bacterial taxa using PICRUSt. Conservation agriculture positively affected taxonomic and functional diversity compared to CP. The agricultural practice was the most important factor in defining the structure of bacterial communities, even more so than rhizosphere and plant growth stage. The rhizosphere enriched fast growing copiotrophic bacteria, such as Rhizobiales, Sphingomonadales, Xanthomonadales, and Burkholderiales, while in the bulk soil of CP other copiotrophs were enriched, e.g., Halomonas and Bacillus. The bacterial community in the maize bulk soil resembled each other more than in the rhizosphere of CA and CP. The bacterial community structure, and taxonomic and functional diversity in the maize rhizosphere changed with maize development and the differences between the bulk soil and the rhizosphere were more accentuated when the plant aged. Although agricultural practices did not alter the effect of the rhizosphere on the soil bacterial communities in the flowering and grain filling stage, they did in the vegetative stage.IMPORTANCE We studied the effect of sustainable conservation agricultural practices versus intensive conventional ones on the soil microbial diversity, potential functionality, and community assembly in rhizosphere of maize cultivated in a semiarid environment. We found that conservation agriculture practices increased the diversity of soil microbial species and functions and strongly affected how they were structured compared to conventional practices. Microbes affected by the roots of maize, the rhizobiome, were different and more diverse than in the surrounding soil and their diversity increased when the plant grew. The agricultural practices affected the maize rhizobiome only in the early stages of growth, but this might have an important impact on the development of maize plant.

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.

Unravelling the genetic and functional diversity of dominant bacterial communities involved in manure co-composting bioremediation of complex crude oil waste sludge

The present study aimed to characterize the bacterial community and functional diversity in co-composting microcosms of crude oil waste sludge amended with different animal manures, and to evaluate the scope for biostimulation based in situ bioremediation. Gas chromatography–mass spectrometry (GC–MS) analyses revealed enhanced attenuation (>90%) of the total polyaromatic hydrocarbons (PAHs); the manure amendments significantly enhancing (up to 30%) the degradation of high molecular weight (HMW) PAHs. Microbial community analysis showed the dominance (>99% of total sequences) of sequences affiliated to phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. The core genera enriched were related to hydrocarbon metabolism (Pseudomonas, Delftia, Methylobacterium, Dietzia, Bacillus, Propionibacterium, Bradyrhizobium, Streptomyces, Achromobacter, Microbacterium and Sphingomonas). However, manure-treated samples exhibited high number and heterogeneity of unique operational taxonomic units (OTUs) with enrichment of additional hydrocarbon-degrading bacterial taxa (Proteiniphilum, unclassified Micrococcales, unclassified Lachnospiraceae, Sphingobium and Stenotrophomonas). Thirty-three culturable hydrocarbon-degrading microbes were isolated from the co-composting microcosms and mainly classified into Burkholderia, Sanguibacter, Pseudomonas, Bacillus, Rhodococcus, Lysinibacillus, Microbacterium, Brevibacterium, Geobacillus, Micrococcus, Arthrobacter, Cellulimicrobacterium, Streptomyces Dietzia,etc,. that was additionally affirmed with the presence of catechol 2,3-dioxygenase gene. Finally, enhanced in situ degradation of total (49%), LMW (>75%) and HMW PAHs (>35%) was achieved with an enriched bacterial consortium of these microbes. Overall, these findings suggests that co-composting treatment of crude oil sludge with animal manures selects for intrinsically diverse bacterial community, that could be a driving force behind accelerated bioremediation, and can be exploited for engineered remediation processes.

Bacterial community structures and functional gene diversity of toluene denitrifying degraders in coking contaminated enrichments

Bacterial community structures and functional gene diversity of toluene denitrifying degraders in coking contaminated enrichments

Anthropogenic activities and seasonal properties jointly drive the assemblage of bacterial communities in subtropical river basins

Anthropogenic activities have inevitably impacted riverine ecosystems, yet their overall contribution to the assemblage of bacterial communities at a large river basin scale remains unclear. In this study, 16S amplicon sequencing was implemented to investigate the bacterial ecosystems in paired water and sediment of North River and West River basins in South China., which contains various anthropogenic environments (e.g., rural/urban area, mining area and livestock area). Subsequently, the links between bacterial community and various types of emerging pollutants in river water were analyzed. The results show that the bacterial assemblage of water and sediment had their own properties that the bacterial community of sediment were mainly affected by seasonal properties, while the bacterial community of water were affected by both seasons and anthropogenic activities. Therein, the aquatic bacterial compositions and abundances were driven by changes in temperature, dissolved oxygen and the emerging pollutants. The dominant phyla Proteobacteria and Firmicutes exhibited adaptability to the mining-affected regions, therein many clades (e.g., Beijerinckiaceae, Acetobacteraceae and Mycobacteriaceae) were also prevalent in the livestock-affected and densely-populated regions. In addition, these two phyla presented associations to the antibiotic resistance in water. The levels of antibiotics, relative antibiotic resistance gens (ARGs) and non-antibiotic pharmaceuticals (NAPs) were closely related to bacterial community composition, diversity and functional diversity, indicating their drive in shifting bacterial communities. Collectively, this work provides a basis for understanding the contribution of anthropogenic activities in shifting bacterial community at a large river basin scale. Further, the results provide new insights for expansion of ecological assessment.

Prediction of bacterial functional diversity in clay microcosms

Microorganisms in clay barriers could affect the long-term performance of waste containers in future deep geological repositories (DGR) for used nuclear fuel through production of corrosive metabolites (e.g., sulfide), which is why clay materials are highly compacted: to reduce both physical space and access to water for microorganisms to grow. However, the highly compacted nature of clays and the resulting low activity or dormancy of microorganisms complicate the extraction of biomarkers (i.e., PLFA, DNA etc.) from such barriers for predictive analysis of microbial risks. In order to overcome these challenges, we have combined culture- and 16S rRNA gene amplicon sequencing-based approaches to describe the functional diversity of microorganisms in several commercial clay products, including two different samples of Wyoming type MX-80 bentonite (Batch 1 and Batch 2), the reference clay for a future Canadian DGR, and Avonlea type Canaprill, a clay sample for comparison. Microorganisms from as-received bentonites were enriched in anoxic 10% w/v clay microcosms for three months at ambient temperature with addition of 10% hydrogen along with presumable indigenous organics and sulfate in the clay. High-throughput sequencing of 16S rRNA gene fragments indicated a high abundance of Gram-positive bacteria of the phylum Firmicutes (82%) in MX-80 Batch 1 incubations. Bacterial libraries from microcosms with MX-80 Batch 2 were enriched with Firmicutes (53%) and Chloroflexi (43%). Firmicutes also significantly contributed (<15%) to the bacterial community in Canaprill clay microcosm, which was dominated by Gram-negative Proteobacteria (>70%). Sequence analysis revealed presence of the bacterial families Peptostreptococcaceae, Clostridiaceae, Peptococcaceae, Bacillaceae, Enterobacteriaceae, Veillonellaceae, Tissierellaceae and Planococcaceae in MX-80 Batch 1 incubations; Bacillaceae, along with unidentified bacteria of the phylum Chloroflexi, in MX-80 Batch 2 clay microcosms, and Pseudomonadaceae, Hydrogenophilaceae, Bacillaceae, Desulfobacteraceae, Desulfobulbaceae, Peptococcaceae, Pelobacteraceae, Alcaligenaceae, Rhodospirillaceae in Canaprill microcosms. Exploration of potential metabolic pathways in the bacterial communities from the clay microcosms suggested variable patterns of sulfur cycling in the different clays with the possible prevalence of bacterial sulfate-reduction in MX-80 bentonite, and probably successive sulfate-reduction/sulfur-oxidation reactions in Canaprill microcosms. Furthermore, analysis of potential metabolic pathways in the bentonite enrichments suggested that bacteria with acid-producing capabilities (i.e., fermenters and acetogens) together with sulfide-producing prokaryotes might perhaps contribute to corrosion risks in clay systems. However, the low activity or dormancy of microorganisms in highly compacted bentonites as a result of severe environmental constraints (e.g., low water activity and high swelling pressure in the confined bentonite) in situ would be expected to largely inhibit bacterial activity in highly compacted clay-based barriers in a future DGR.