Distinct bacterial community structure, assembly and functions between aged and multiple petroleum-contaminated sites

Dependence of soil microbial community structure and function on land use types and management regimes

Soils present a limited resource for agricultural production and bear a vast diversity of organisms crucial for crop health and the provision of ecosystem services. There is growing evidence that agricultural practices affect soil microbial community structure and function but currently, there is a knowledge gap when it comes to tropical arable farming systems. In this study, we investigated the long-term impact of organic and conventional production systems on bacterial communities in two field trial located on a rhodic and humic nitisol in the Central Highlands of Kenya. The field sites operate on a full factorial design, testing farming systems (organic vs conventional) and input levels (high vs low). Including four field replication we assessed soil bacterial community structure via amplicon sequencing of the 16S rRNA gene and soils capacity for nitrification and nitrous oxide reduction via qPCR of functional genes (bacterial and archaeal amoA, nosZ) after 12 years of distinct management and before the start of the 5th three-year crop rotation period in 2019. The abundances of amoA bearing nitrifiers and nosZ bearing nitrous oxide reducers were enhanced in the high input organic production system on humic but not in rhodic nitisols. For both soil types, high input organic production system resulted in distinct bacterial community structure with enhanced bacterial richness compared to conventional and low input production systems. In rhodic and humic nitisols 160 and 84 OTUs were found to be indicative for organic production system at high input levels organic. Taxa associated with this system were identified as potential primary decomposers or symbionts related to plant nitrogen fixation, suggesting organic fertilization strategies such as manure composting as major driver for changes in soil bacterial community structure. This study reveals that organic production systems at high input levels on tropical nitisols translates to distinct soil bacterial communities with increased capacity for soil processes that are crucial for crop nutrient supply.

The rapid decline of sea ice in the relatively understudied Central Arctic Ocean has a significant impact on bacterial biodiversity and the ecological functions they support. We investigated the bacterial community composition and the associated metabolic functions from three geographically distinct sea-ice floes: first-year ice (FYI) at the North Pole and western Nansen Basin and second-year or multi-year ice (SYI/MYI) in the western Amundsen Basin. We resolved the sea-ice bacterial community diversity at species-level precision using a long-read amplicon (n = 18) and metagenomic (n = 3) sequencing approach. The amplicon sequencing highlighted marked differences in bacterial community structure driven by ice age, floe origin, and environmental factors, demonstrating pronounced vertical structuring among ice horizons. Bacterial taxa like Paraglaciecola psychrophila, Hydrogenophaga crassostreae, Octadecabacter arcticus, and Polaribacter irgensii mainly dominated the bottom layers of SYI/MYI, whereas species Actimicrobium antarcticum, Polaromonas cryoconiti, O. antarcticus, and Rhodoferax sp. dominated the FYI. Similarly, notable taxonomic differences were observed in bacterial taxa inhabiting the surface and interior layers of FYI and SYI/MYI (e.g., F. frigoris and Hydrogenophaga sp.). The metagenomic analysis showed the prevalence of sulfur cycling-associated (assimilatory and dissimilatory sulfur metabolism) and complex carbon degradation processes in sea ice. We also elucidated the potential ecological role of novel metagenome-assembled genomes belonging to the genus Aquiluna through phylogenomic and pangenomic analyses. Overall, our findings revealed novel insights on the distinct bacterial communities that inhabit ice horizons and their associated ecological functions correlating with sea-ice type, origin, and habitat characteristics in the Central Arctic Ocean.IMPORTANCEThe Arctic region is warming nearly four times faster than the global average, leading to the continuous replacement of its thick multi-year sea ice with thinner first-year ice. The reduction in Arctic sea-ice cover was previously shown to have cascading effects on sea-ice-associated microbial communities and their role in the functioning of the ecosystem. This study provides the first high-resolution, species-level insight into the bacterial community composition and metabolic potential across different sea-ice types in the Central Arctic Ocean-an understudied yet rapidly changing environment. By combining long-read amplicon and metagenomic sequencing, we uncover distinct bacterial assemblages and functional metabolic roles that were shaped by the ice age and other physicochemical properties. Our findings highlight the ecological importance of sea-ice associated bacterial communities and the prevalence of sulfur metabolism and carbon degradation processes in different sea-ice types found in the central Arctic Ocean through genome-resolved metagenomics.

Lycium ruthenicum, a halophytic shrub, has been used to remediate saline soils in northwest China. However, little is known about its root-associated microbial community and how it may be affected by the plant’s growth cycle. In this study, we investigate the microbial community structure of L. ruthenicum by examining three root compartments (rhizosphere, rhizoplane, and endosphere) during four growth stages (vegetative, flowering, fruiting, and senescence). The microbial community diversity and composition were determined by Illumina MiSeq sequencing of the 16S V3–V4 and 18S ITS regions. Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, and Acidobacteria were the dominant bacterial phyla, while Ascomycota, Basidiomycota, and Mortierellomycota were the most dominant fungal phyla. The alpha diversity of the bacterial communities was highest in the rhizosphere and decreased from the rhizosphere to the endosphere compartments; the fungal communities did not show a consistent trend. The rhizosphere, rhizoplane, and endosphere had distinct bacterial community structures among the three root compartments and from the bulk soil. Additionally, PERMANOVA indicated that the effect of rhizocompartments explained a large proportion of the total community variation. Differential and biomarker analysis not only revealed that each compartment had unique biomarkers and was enriched for specific bacteria, but also that the biomarkers changed with the plant growth cycle. Fungi were also affected by the rhizocompartment, but to a much less so than bacteria, with significant differences in the community composition along the root compartments observed only during the vegetative and flowering stages. Instead, the growth stages appear to account for most of the fungal community variation as demonstrated by PCoA and NMDS, and supported by differential and biomarker analysis, which revealed that the fungal community composition in the rhizosphere and endosphere were dynamic in response to the growth stage. Many enriched OTUs or biomarkers that were identified in the root compartments were potentially beneficial to the plant, meanwhile, some harmful OTUs were excluded from the root, implying that the host plant can select for beneficial bacteria and fungi, which can promote plant growth or increase salt tolerance. In conclusion, the root compartment and growth stage were both determinant factors in structuring the microbial communities of L. ruthenicum, but the effects were different in bacteria and fungi, suggesting that bacterial and fungal community structures respond differently to these growth factors.

Phytoplankton have been observed to be widely distributed in the oceanic vertical water columns and have an important contribution to carbon sequestrationviabiological pump mechanism. However, in seamount areas with strong hydrodynamics, their vertical export is still unclear. Moreover, considering phyto- and bacterioplankton are inseparable in the ocean, their correlation in the water columns is also an important scientific issue to be understood, which is related to the microbial ecological process in the aphotic zone. Here, we revealed that there were various phytoplankton (< 20 µm) along a deep-sea seamount (M5 seamount) in the Western Pacific Ocean, and their molecular community structures had no significant difference in different water layers, which were all dominated by Dinophyceae, Syndiniales, and Baciilariophyta. In contrast, the vertical distribution of bacterioplankton community structure showed great variation. Notably, distinct species-specific algae-bacteria relationships occurred in different water layers, and relatively more prominent algae-bacteria relationships occurred in the mesopelagic and bathypelagic zones than the euphotic zone. In laboratory experiments, after co-cultivating the significantly different bacterial communities from different water layers withSynechococcussp. PCC7002 andPhaeodactylum tricornutumCCMP2561, respectively, the distinct bacterial community structures from different water layers turned similar, reflecting the strong reshaping effect of phytoplankton on the structure of bacterial communities. However, the reshaping effects on bacterial communities by the two algae differed significantly. Overall, the vertically transported phytoplankton in the seamount area not only contribute importantly to carbon sequestrationviabiological pump, but also may have an important reshaping effect on the bacterioplankton community structure in different water layers.

IntroductionMicroorganisms, which are ubiquitous in the environment, have evolved a diverse array of arsenic biotransformation genes (ABGs). Dust harbors a wide range of microorganisms. However, the distinct characteristics of bacterial community structures and ABG profiles in dust, compared with those in other environments such as soil and water, remain poorly understood.MethodsIn this study, dust samples were simultaneously collected alongside surrounding soil and seawater samples in Xiamen, a coastal city of China, to investigate the distinct profiles and potential sources of bacterial communities and ABGs in dust using 16S rRNA gene amplicon sequencing and metagenomic sequencing.Results and discussionAbundant and diverse bacterial communities and ABGs were detected in dust, revealing significant differences in community structures and ABG profiles compared with those in soil and seawater. Soil was identified as the primary source for both bacterial communities and ABGs in dust through fast expectation–maximization microbial source tracking (FEAST). Acetobacteraceae, which showed significantly greater relative abundance (p < 0.001) in dust than in soil and seawater, was also identified as a keystone taxon in the dust bacterial co-occurrence network. Furthermore, metagenome-assembled genomes (MAGs) affiliated with Acetobacteraceae were effectively recovered from dust via metagenomic binning, and these MAGs harbored an array of ABGs, indicating that Acetobacteraceae could be important hosts for ABGs in dust. Overall, our findings offer new insights into bacterial communities and ABGs in dust, thereby improving our understanding of arsenic biogeochemical cycling.

Differences in bacterial community structure and potential functions among Eucalyptus plantations with different ages and species of trees

Unique hyper-thermal composting process in Kagoshima City forms distinct bacterial community structures

Compared to planktonic bacterial populations, biofilms have distinct bacterial community structures and play important ecological roles in various aquatic environments. Despite their ecological importance in nature, bacterial community structure and its succession during biofilm development in the Antarctic marine environment have not been elucidated. In this study, the succession of bacterial community, particularly during the early stage of biofilm development, in the Antarctic marine environment was investigated by pyrosequencing of the 16S rRNA gene. Overall bacterial distribution in biofilms differed considerably from surrounding seawater. Relative abundance of Gammaproteobacteria and Bacteroidetes which accounted for 78.9–88.3% of bacterial community changed drastically during biofilm succession. Gammaproteobacteria became more abundant with proceeding succession (75.7% on day 4) and decreased to 46.1% on day 7. The relative abundance of Bacteroidetes showed opposite trend to Gammaproteobacteria, decreasing from the early days to the intermediate days and becoming more abundant in the later days. There were striking differences in the composition of major OTUs (≥ 1%) among samples during the early stages of biofilm formation. Gammaproteobacterial species increased until day 4, while members of Bacteroidetes, the most dominant group on day 1, decreased until day 4 and then increased again. Interestingly, Pseudoalteromonas prydzensis was predominant, accounting for up to 67.4% of the biofilm bacterial community and indicating its important roles in the biofilm development.

Conversion of vegetable wastes to organic acids in leaching bed reactor: Performance and bacterial community analysis

Litter decomposition is a key step in global biogeochemical cycling. In forest ecosystems, litter from different tree spec1ies often decompose together. Although species diversity is widely acknowledged to accelerate decomposition through the regulation of nutrient transfer between litter and decomposer communities, the underlying mechanism remains unclear. To explore the association between the bacterial community and mixed-litter chemical transformation, we conducted a one-year litter mixing decomposition experiment using leaf litter from four dominant tree species in Mount Tai (Eastern China), Robinia pseudoacacia, Quercus acutissima, Pinus tabulaeformis, and Pinus densiflora. Our results showed that: 1) Mass loss of leaf litter mixtures was significantly faster than that of leaf litter monocultures, except for R. pseudoacacia. Litter mixtures without R. pseudoacacia showed non-additive synergistic effects, whereas litter mixtures with R. pseudoacacia exerted additive effects; 2) Litter species in the absence of R. pseudoacacia significantly decreased the nutrient retention rates of litter mixtures compared to those of monocultures; 3) Litter mixtures with or without R. pseudoacacia showing additive and non-additive effects in monocultures had a distinct bacterial community structure; 4) Bacterial community structure was also modified by initial litter traits; carbon (C), nitrogen (N), and phosphorus (P) concentrations in monocultures; N/P and C/N ratios of mixtures with R. pseudoacacia; and the lignin/N ratio of mixtures without R. pseudoacacia. Overall, these findings indicate that tree species diversity controls decomposition and nutrient cycling, implying that an appropriate species community composition is beneficial to maintaining forest ecosystems.

Stream bacterial diversity peaks at intermediate freshwater salinity and varies by salt type

Soil microbial communities represent the largest biodiversity on Earth, holding an important role in promoting plant growth and productivity. However, the knowledge about how soil factors modulate the bacteria community structure and distribution in tropical regions remain poorly understood, mainly in different cowpea producing ecoregions belonging to Northeastern Brazil. This study addressed the bacterial community along three different ecoregions (Mata, Sertão, and Agreste) through the16S rRNA gene sequencing. The results showed that soil factors, such as Al3+, sand, Na+, cation exchange excel, and total organic C, influenced the bacterial community and could be a predictor of the distinct performance of cowpea production. Also, the bacterial community changed between different ecoregions, and some keystone groups related to plant-growth promotion, such as Bradyrhizobium, Bacillales, Rhizobiales, and Solibacillus, were correlated to cowpea yield, so revealing that the soil microbiome has a primordial role in plant productivity. Here, we provide evidence that bacterial groups related to nutrient cycling can help us to increase cowpea efficiency and we suggest that a better microbiome knowledge can contribute to improving the agricultural performance.

Glaciated alpine floodplains are responding quickly to climate change through shrinking ice masses. Given the expected future changes in their physicochemical environment, we anticipated variable shifts in structure and ecosystem functioning of hyporheic microbial communities in proglacial alpine streams, depending on present community characteristics and landscape structures. We examined microbial structure and functioning during different hydrologic periods in glacial (kryal) streams and, as contrasting systems, groundwater-fed (krenal) streams. Three catchments were chosen to cover an array of landscape features, including interconnected lakes, differences in local geology and degree of deglaciation. Community structure was assessed by automated ribosomal intergenic spacer analysis and microbial function by potential enzyme activities. We found each catchment to contain a distinct bacterial community structure and different degrees of separation in structure and functioning that were linked to the physicochemical properties of the waters within each catchment. Bacterial communities showed high functional plasticity, although achieved by different strategies in each system. Typical kryal communities showed a strong linkage of structure and function that indicated a major prevalence of specialists, whereas krenal sediments were dominated by generalists. With the rapid retreat of glaciers and therefore altered ecohydrological characteristics, lotic microbial structure and functioning are likely to change substantially in proglacial floodplains in the future. The trajectory of these changes will vary depending on contemporary bacterial community characteristics and landscape structures that ultimately determine the sustainability of ecosystem functioning.

Increases in bacterial community network complexity induced by biochar-based fertilizer amendments to karst calcareous soil