Shaping Bacterial Communities Research Articles

Experimentally determined traits shape bacterial community composition one and five years following wildfire.

Wildfires represent major ecological disturbances, burning 2-3% of Earth's terrestrial area each year with sometimes drastic effects above- and belowground. Soil bacteria offer an ideal, yet understudied system within which to explore fundamental principles of fire ecology. To understand how wildfires restructure soil bacterial communities and alter their functioning, we sought to translate aboveground fire ecology to belowground systems by determining which microbial traits are important post-fire and whether changes in bacterial communities affect carbon cycling. We employed an uncommon approach to assigning bacterial traits, by first running three laboratory experiments to directly determine which microbes survive fires, grow quickly post-fire and/or thrive in the post-fire environment, while tracking CO2 emissions. We then quantified the abundance of taxa assigned to each trait in a large field dataset of soils one and five years after wildfires in the boreal forest of northern Canada. We found that fast-growing bacteria rapidly dominate post-fire soils but return to pre-burn relative abundances by five years post-fire. Although both fire survival and affinity for the post-fire environment were statistically significant predictors of post-fire community composition, neither are particularly influential. Our results from the incubation trials indicate that soil carbon fluxes post-wildfire are not likely limited by microbial communities, suggesting strong functional resilience. From these findings, we offer a traits-based framework of bacterial responses to wildfire.

Slope gradient altered microbial community composition in the sloping cropland in black soil

Soil microorganisms are the main driving force in ecological and biogeochemical processes, such as carbon mineralization, humus formation, and nutrient cycles. Soil erosion may dramatically alter microbial properties. In hilly areas, soil erosion is highly attributed to topographic properties such as slope position and gradient. However, it is still unclear how slope position and gradient affects soil microbial characteristics. Herein, we compared the soil microbial characteristics in the sloping cropland between different slope gradients (0°–1.5°, 3°–5°, >5°) and positions (top, middle, and bottom) in the typical black soil area of Northeast China. The results indicated that slope gradient significantly influenced soil clay content, water stable aggregate, organic matter, available potassium, total dissolved nitrogen and pH. In comparison, slope position had no noticeable impact on the physical or chemical properties. Results showed that Proteobacteria, Acidobacteria, Gemmatimonadetes, Planctomycetes, and Actinobacteria comprise 92 % of all phyla, whereas the top five bacterial families and genera account for 72 % and 50 % of the bacterial sequences, respectively. Ascomycota, Basidiomycota, and Chytridiomycota made up 83 % of the phyla, and the top five families and genera made up 43 % and 31 %, respectively, of the entire fungi sequence. Microbial alpha diversity (bacteria and fungi) was similar among the slope gradients and slope positions. The bacterial and fungal community composition was only affected by the slope gradient, with the highest slope gradient having a significantly lower value than other levels. Based on RDA analysis, water stable aggregate, clay content, organic matter, available nitrogen and cation exchange capacity concentration appeared to be the most critical factors in shaping bacterial and fungal communities. This study suggests that slope gradient but not slope position might be the main topographic factor decreasing microbial community composition in the sloped cropland area.

Both host and diet shape bacterial communities of predatory mites.

Microbial communities, derived from food, ambient, and inner, can affect host ecological adaption and evolution. Comparing with most phytophagous arthropods, predators may have more opportunities to develop specific microbiota depending on the level of prey specialization. To explore how diet sources affect host microbial communities and vary across predator species, we considered 3 types of predators from Phytoseiidae (Acari: Mesostigmata): polyphagous (Amblyseius orientalis Ehara, Neoseiulus barkeri Hughes, and Amblyseius swirskii Athias-Henrio), oligophagous (Neoseiulus californicus McGregor), and monophagous (Phytoseiulus persimilis Athias-Henriot) predatory mites. The polyphagous species were fed on 2 types of diets, natural prey and alternative prey. By using 16S rRNA sequencing, we found that diet was the main source of microbiota in predatory mites, while there was no clear pattern affected by prey specialization. Among 3 polyphagous predators, host species had a larger impact than prey on microbial composition. Unlike A. orientalis or N. barkeri which showed consistency in their microbiota, prey switching significantly affected β-diversity of bacterial composition in A. swirskii, with 56% of the microbial alteration. In short, our results confirmed the substantial influence of diet on host microbial construction in predatory species, and highlighted species differences in shaping the microbiota which are not necessarily related to prey specialization.

Mineral-solubilizing microbial inoculant positively affects the multifunctionality of anthropogenic soils in abandoned mining areas

The mining industry has a significant negative impact on ecosystems, and the remediation of abandoned mining sites requires effective strategies. One promising approach is the incorporation of mineral-solubilizing microorganisms into current external soil spray seeding technologies. These microorganisms possess the ability to decrease mineral particle sizes, promote plant growth, and enhance the release of vital soil nutrients. However, most previous studies on mineral-solubilizing microorganisms have been conducted in controlled greenhouse environments, and their practical application in field settings remains uncertain. To address this knowledge gap, we conducted a four-year field experiment at an abandoned mining site to investigate the efficacy of mineral-solubilizing microbial inoculants in restoring derelict mine ecosystems. We assessed soil nutrients, enzyme activities, functional genes, and soil multifunctionality. We also examined microbial compositions, co-occurrence networks, and community assembly processes. Our results demonstrated that the application of mineral-solubilizing microbial inoculants significantly enhanced soil multifunctionality. Interestingly, certain bacterial phyla or class taxa with low relative abundances were found to be key drivers of multifunctionality. Surprisingly, we observed no significant correlation between microbial alpha diversity and soil multifunctionality, but we did identify positive associations between the relative abundance and biodiversity of keystone ecological clusters (Module #1 and #2) and soil multifunctionality. Co-occurrence network analysis revealed that microbial inoculants reduced network complexity while increasing stability. Additionally, we found that stochastic processes played a predominant role in shaping bacterial and fungal communities, and the inoculants increased the stochastic ratio of microbial communities, particularly bacteria. Moreover, microbial inoculants significantly decreased the relative importance of dispersal limitations and increased the relative importance of drift. High relative abundances of certain bacterial and fungal phyla were identified as major drivers of the microbial community assembly process. In conclusion, our findings highlight the crucial role of mineral-solubilizing microorganisms in soil restoration at abandoned mining sites, shedding light on their significance in future research endeavors focused on optimizing the effectiveness of external soil spray seeding techniques.

Bioaugmentation of woodchip bioreactors by Pseudomonas nicosulfuronedens D1-1 with functional species enrichment

A novel heterotrophic nitrification and aerobic denitrification (HN-AD) bacterium D1-1 was identified as Pseudomonas nicosulfuronedens D1-1. Strain D1-1 removed 97.24%, 97.25%, and 77.12% of 100 mg/L NH4+-N, NO3−-N, and NO2−-N, with corresponding maximum removal rates of 7.42, 8.69, and 7.15 mg·L−1·h−1, respectively. Strain D1-1 bioaugmentation enhanced woodchip bioreactor performance with an average NO3−-N removal efficiency of 93.8%. Bioaugmentation enriched N cyclers along with increased bacterial diversity and predicted genes for denitrification, DNRA (dissimilatory nitrate reduction to ammonium), and ammonium oxidation. It also reduced local selection and network modularity from 4.336 to 0.934, resulting in predicted nitrogen (N) cycling genes shared by more modules. These observations suggested that bioaugmentation could enhance the functional redundancy to stabilize the NO3−-N removal performance. This study provides insights into the potential applications of HN-AD bacteria in bioremediation or other environmental engineering fields, relying on their ability to shape bacterial communities.

Symbiont Cardinium and host-environment factors shape bacterial communities in spider mites

Symbiont Cardinium and host-environment factors shape bacterial communities in spider mites

Habitats shape root-associated fungal and bacterial communities of Minjiang fir saplings

Habitats shape root-associated fungal and bacterial communities of Minjiang fir saplings

Assembly processes, driving factors, and shifts in soil microbial communities across secondary forest succession

AbstractSecondary forest succession after clear‐cutting is one of the foremost ecosystem restoration strategies, while soil microbes play essential roles in the processes by modulating nutrient cycling. However, the assembly processes and driving factors of soil microbial communities across secondary forest succession remain unclear. Here, we studied the assembly processes of soil microbial communities and examined shifts in soil microbial community‐associated functional dynamics across secondary forest succession. Our results showed that the stochastic process was more important in shaping bacterial community assembly throughout the successional process [modified stochasticity ratio (MST) > 50%], while the fungal community assembly was initially governed by deterministic processes (MST < 50%), but there was a progressive increase in stochastic selection as succession proceeded. Soil organic carbon and pH were principal factors for the explanation of changes in the bacterial community structure (total explained 43% change), and tree richness and productivity were principal factors for the explanation of shifts in the fungal community structure (total explained 17% change). The relative abundance of nitrogen transformation and saprotroph functional groups increased gradually with succession, whereas ectomycorrhizal fungi significantly declined. The results suggested that microbial community succession might accelerate the soil carbon and nitrogen turnover rates. Used together, the mechanisms shaping fungal and bacterial community structure are different in secondary forest succession and highlight that those fungi and bacteria are primarily controlled by plant traits and soil properties, respectively. Variations in microbial functional groups provide new insight into the mechanisms underlying the soil microbe‐driven soil nutrient cycles during secondary forest succession.

The role of inherited characteristics from parent materials in shaping bacterial communities in agricultural soils

Parent materials are crucial in soil formation and development, but their importance in shaping soil bacterial communities after thousands of years of soil formation remains unknown, especially in agricultural soils. To resolve the influence of underlying features inherited from parent materials on soil microbiome, the microbial community in 197 agricultural soils with long-term crop cultivation history and nonagricultural reference soils from four major types of soils in China, i.e., quaternary red clay soils, tertiary red sandstone soils, alluvial soils and black soils, were analyzed and compared. We found that different types of soils supported distinct bacterial communities. The characteristics inherited from parent materials explained more of the variation (31.47%) in bacterial community structure than the selected variables regulated by soil management (1.63%) and the climate condition (1.10%). Only 9.0% of total bacterial amplicon sequence variants (ASVs) which contributed, on average, 47% of the total bacterial abundances in a given agricultural soil, were shared by all soil types. These abundant common ASVs were closely related to agricultural practices, suggesting a strong enrichment effect of a small number of core taxa by long-term crop cultivation. In contrast, approximately 55.6% of ASVs with low relative abundance were specific to soil type. These specific groups were closely associated with the distinctive features of soil type, implying that they represent unique populations selected by the parent material features during pedogenesis. Collectively, soil type may have a strong selective pressure on the bacterial communities in matured agricultural soils, leading to a large pool of specific taxa with limited environmental occurrence. Whilst a small number of core taxa achieve high abundances by responding to long-term crop cultivation.

Colonization order of bacterial isolates on treefrog embryos impacts microbiome structure in tadpoles.

Priority effects, or impacts of colonization order, may have lasting influence on ecological community composition. The embryonic microbiome is subject to stochasticity in colonization order of bacteria. Stochasticity may be especially impactful for embryos developing in bacteria-rich environments, such as the embryos of many amphibians. To determine if priority effects experienced as embryos impacted bacterial community composition in newly hatched tadpoles, we selectively inoculated the embryos of laboratory-raised hourglass treefrogs, Dendropsophus ebraccatus, with bacteria initially isolated from the skin of wild D. ebraccatus adults over 2 days. First, embryos were inoculated with two bacteria in alternating sequences. Next, we evaluated the outcomes of priority effects in an in vitro co-culture assay absent of host factors. We then performed a second embryo experiment, inoculating embryos with one of three bacteria on the first day and a community of five target bacteria on the second. Through 16S rRNA gene amplicon sequencing, we observed relative abundance shifts in tadpole bacteria communities due to priority effects. Our results suggest that the initial bacterial source pools of embryos shape bacterial communities at later life stages; however, the magnitude of those changes is dependent on the host environment and the identity of bacterial colonists.

Application of bio-slow sand filters for drinking water production: Linking purification performance to bacterial community and metabolic functions

Bio-slow sand filters (BSSFs) are widely employed in rural drinking water treatment ascribing to its economic applicability, easy operation and high efficiency. This study investigated the influence of particle size, filter thickness, water quality and filtration rate on decontamination performance, bacterial community and metabolic function of BSSFs. The effluent ammonia nitrogen during stable operation period basically met the standards for drinking water quality in China (0.5 mg/L). The average removal efficiencies of fine sand were about 4 % higher than those of coarse sand, and thick filter layer showed more stable performance. Schmutzdecke removed most turbidity and organic pollutants, playing an overwhelming role in water purification. Filtration rate was a key factor in shaping bacterial community structure. Proteobacteria and Cyanobacteria were dominant phyla, whose relative abundance significantly decreased and increased as filtration rate increasing, respectively. Co-occurrence patterns were dominant within bacterial communities. Function bacteria (e.g. Hyphomicrobium and Methylophilus) and rare genera (Curvibacter and Simplicispira) were identified as hub genera in the networks. The bacterial communities exhibited a metabolic versatility. Several pathways for secondary metabolism significantly shifted under different conditions, such as xenobiotics biodegradation and metabolism. Moreover, filtration rate and dominant genera greatly affected pollutant removal performance. Many species of Proteobacteria and Bacteroidota were closely related to carbohydrate metabolism, energy metabolism and nucleotide metabolism, and metabolic functions corresponded more cohesively to conditional abundant taxa, conditional rare or abundant taxa, conditional rare taxa. This study highlights the adaptability and bacterial community characteristics of BSSFs, and provides references for their practical application.

Weathering extents and anthropogenic influences shape the soil bacterial community along a subsurface zonation

Subsurface environments are composed of various active soil layers with dynamic biogeochemical interactions. We investigated soil bacterial community composition and geochemical properties along a vertical soil profile, which was categorized into surface, unsaturated, groundwater fluctuated, and saturated zones, in a testbed site formerly used as farmland for several decades. We hypothesized that weathering extent and anthropogenic inputs influence changes in the community structure and assembly processes and have distinct contributions along the subsurface zonation. Elemental distribution in each zone was strongly affected by the extent of chemical weathering. A 16S rRNA gene analysis indicated that bacterial richness (alpha diversity) was highest in the surface zone, and also higher in the fluctuated zone, than in unsaturated and saturated zones due to the effects of high organic matter, high nutrient levels, and/or aerobic conditions. Redundancy analysis showed that major elements (P, Na), a trace element (Pb), NO3, and the weathering extent were key driving forces shaping bacterial community composition along the subsurface zonation. Assembly processes were governed by specific ecological niches, such as homogeneous selection, in the unsaturated, fluctuated, and saturated zones, while in the surface zone, they were dominated by dispersal limitation. These findings together suggest that the vertical variation in soil bacterial community assembly is zone-specific and shaped by the relative influences of deterministic vs. stochastic processes. Our results provide novel insights into the relationships between bacterial communities, environmental factors, and anthropogenic influences (e.g., fertilization, groundwater, soil contamination), and into the roles of specific ecological niches and subsurface biogeochemical processes in these relationships.

Contributions of carbon source, crop cultivation, and chemical property on microbial community assemblage in soil subjected to reductive disinfestation.

In agricultural practice, reductive soil disinfestation (RSD) is an effective method for eliminating soil-borne pathogens that depends heavily on carbon source. However, knowledge regarding the assembly of soil microbial communities in RDS-treated soils amended with different carbon sources after continuous crop cultivation is still not well-characterized. RSD treatments were performed on greenhouse soil with six different carbon sources (ethanol, glucose, alfalfa, wheat bran, rice bran, and sugarcane residue), which have different C:N ratios (Org C/N) and easily oxidized carbon contents (Org EOC). After RSD, two consecutive seasons of pepper pot experiments were conducted. Then, the effects of carbon source property, crop cultivation, and soil chemical property on soil microbial community reestablishment, pathogen reproduction, and crop performance were investigated in the RSD-cropping system. Variation partition analysis indicated that carbon source property, crop cultivation, and soil chemical property explained 66.2 and 39.0% of bacterial and fungal community variation, respectively. Specifically, Mantel tests showed that Org C/N, crop cultivation, soil available phosphorus and potassium were the most important factors shaping bacterial community composition, while Org C/N, Org EOC, and crop cultivation were the most important factors shaping fungal community composition. After two planting seasons, the number of cultivable Fusarium was positively correlated with Org EOC, and negatively correlated with soil total organic carbon, Fungal Chao1, and Fungal PC1. Crop yield of complex-carbon soils (Al, Wh, Ri and Su) was negatively affected by Org C/N after the first season, and it was highest in Al, and lower in Et and Su after the second season. Overall, Org EOC and Org C/N of carbon source were vitally important for soil microbe reestablishment, Fusarium reproduction and crop performance. Our findings further broaden the important role of carbon source in the RSD-cropping system, and provide a theoretical basis for organic carbon selection in RSD practice.

Diversity and Potential Interactions of Soil Viruses and Host Bacteria under Different Land Use Patterns

Viruses, as the most abundant entities on earth, play an important role in shaping bacterial communities, mediating gene transfer between host cells, and promoting biogeochemical cycles. Yet, soil viruses remain understudied, as there is a lack of information about the mechanisms of community construction, interactions between viruses and host bacteria, and ecological functions. To expand our understanding of soil viruses, we investigated six viromes across three land use types in northeast and southwestern China, including agricultural and forest soils. We analyzed viral and bacterial community composition and explored their interactions. We utilized metagenomic sequencing technology and high-throughput 16S rRNA gene sequencing to study viral and bacterial communities. Twenty-four viral families were detected in six viromes including sixteen dsDNA virus families and eight ssDNA virus families. Viral and bacterial communities were significantly different between various land use types, with viruses having greater disparities. The composition of bacterial communities in soils across different land use types was inconsistent with their viral communities. We identified abundant auxiliary carbohydrate-active enzyme genes from viromes. The results revealed that soil viral communities differ by land use type and that viruses could regulate bacterial carbon cycling processes by encoding auxiliary metabolic genes.

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.

Abundant and rare bacteria in anthropogenic estuary: Community co-occurrence and assembly patterns

In estuary, bacteria are critically vital to ecosystem function and sustainability. However, the effect of geographic distance and its related factors (i.e., salinity and nutrients) on bacterial diversity, co-occurrence, as well as community assembly on the abundant and rare species scale remained to be discussed. In this study, we deciphered the bacterial dynamics and ecological processes in the anthropogenic estuary of the Haihe River, in China. The results revealed that salinity was the major abiotic factor to shape bacterial community composition, diversity, and network complexity, and the role of biotic cytometric characteristics was considerable as well. Furthermore, the salinity gradient tended to select bacteria with low nucleic acid (LNA) such as Candidatus Pelagibacter and Longivirga, and abundant bacteria were more sensitive to the salinity gradient in comparison with rare ones. The similar keystone number and network topology values indicated that both abundant and rare bacteria played important ecological functions in degrading pollutants, developing co-occurrence networks, and maintaining compositional stability and complexity. In addition, drift and dispersion limitation dominated the ecological processes in the community assembly, suggesting that although salinity caused the migration of species, its ecological role was still weaker than that of stochastic processes. Further, niche differentiation contributed to different stochastic components of abundant and rare species. In high-salinity areas, rare bacteria with small population sizes but high diversity were enriched, which made the bacterial community more affected by ecological drift. Our study illustrated the different responses of abundant and rare bacteria to salinity and the assembly process of bacterial communities in anthropogenic estuary, deepening the understanding of their ecological processes in the estuarine ecosystem.

Effects of land-use intensity, grazing and fire disturbances on soil bacterial and fungal communities in subtropical wetlands

Bacteria and fungi are primary components in wetland soil microbial communities and provide essential ecosystem functions and services. Understanding responses of bacterial and fungal communities to multiple drivers of environmental change and their interactions is crucial for wetland conservation and management, particularly for those embedded in agricultural landscapes. Yet little is known about effect of agricultural land use and wetland management on soil microbial communities in subtropical seasonal wetlands. Here, we used a long-term whole-ecosystem wetland experiment to examine individual and interactive effects of upland land-use intensification, livestock grazing, and prescribed fire on soil bacteria and fungi. We asked: (1) How do land-use intensification, grazing and fire disturbances interact to alter taxonomic composition and functional potential of wetland soil bacterial and fungal communities? (2) To what extent would these management and disturbance effects on wetland microbial communities manifest through alterations in soil properties? Our results showed that both microbial taxonomic and functional composition are responsive to agricultural land use and wetland management. Upland land-use intensification was the strongest driver (as compared to fire and grazing) in shaping bacterial and fungal community composition. Specifically, land-use intensification increased functional richness of both bacteria and fungi, whereas grazing and fire only interactively affected bacterial functional richness. In addition, responses of bacterial and fungal species diversity to wetland management varied, where grazing and fire reduced fungal species diversity in wetlands embedded in low-intensity managed pastures, but none of these management practices altered bacterial species diversity. Further, we found that pH and secondary nutrients (i.e., Ca and Mg) availability were the most important soil properties that explain how agricultural land use and wetland management drive the composition of bacterial and fungal communities. Our findings suggest that integration of lime application into intensified land uses to neutralize soil pH could facilitate maintenance of microbial diversity and associated functions. Our results highlight the need to comprehensively assess management impacts on soil microorganisms, rather than using a single or few indicators, due to inconsistent responses of bacterial and fungal communities, as well as their varied taxonomic and functional responses.

Efficient H2 production in a ZnFe2O4/g-C3N4 photo-cathode single-chamber microbial electrolysis cell.

Photo-assisted single-chamber microbial electrolysis cells (MECs) incorporating semiconductor cathodes are attractively promising for exclusive hydrogen without CH4 and CO2. However, the unsustainable, high cost, and unstable metal catalysts on the cathodes along with the intricacies behind the interplay of circuital current, light illumination, and bacterial communities on both electrodes are poorly understood. Herein, photo-assisted single-chamber MECs incorporating ZnFe2O4/g-C3N4 cathodes are demonstrated to achieve efficient production of exclusive hydrogen (0.11 ± 0.01 m3/m2/day; 1.70 ± 0.04 m3/m3/day) with a solar-to-hydrogen conversion efficiency of 4.08 ± 0.17% and an energy efficiency relative to electrical input of 233 ± 5%. The ZnFe2O4/g-C3N4 structured cathodes exhibited appreciable higher photocurrents than the controls (g-C3N4: 4.3-fold; ZnFe2O4: 3.3-fold), and negligible leaking of Fe and Zn after the 4th-cycle operation. Circuital current and light illumination were proven to varying degree shape both electrodes for building up functional bacterial communities with metabolic regulation at the prolonged operation of 12 batch cycles. Energy metabolism and carbohydrate metabolism along with membrane transport, signal transduction, and cell motility based on PICRUSt functional prediction further confirmed the photo-assisted single-chamber MECs for efficient hydrogen production. This study provided a sustainable, cost-effective, and efficient approach for achieving high rates of exclusive hydrogen production and offered new insights for ingenious interplay of circuital current, light illumination, and bacterial communities for efficient hydrogen production in the photo-assisted single-chamber MECs. KEY POINTS: • ZnFe2O4/g-C3N4 cathodes of single-chamber MECs achieve efficient H2 production. • Light irradiation and circuit current shape bacterial communities on both electrodes. • Circuital current contributes to less leaking of Fe and Zn, and thus system stability.

Environmental micro-niche filtering shapes bacterial pioneer communities during primary colonization of a Himalayas' glacier forefield.

The pedogenesis from the mineral substrate released upon glacier melting has been explained with the succession of consortia of pioneer microorganisms, whose structure and functionality are determined by the environmental conditions developing in the moraine. However, the microbiome variability that can be expected in the environmentally heterogeneous niches occurring in a moraine at a given successional stage is poorly investigated. In a 50 m2 area in the forefield of the Lobuche glacier (Himalayas, 5050 m above sea level), we studied six sites of primary colonization presenting different topographical features (orientation, elevation and slope) and harbouring greyish/dark biological soil crusts (BSCs). The spatial vicinity of the sites opposed to their topographical differences, allowed us to examine the effect of environmental conditions independently from the time of deglaciation. The bacterial microbiome diversity and their co-occurrence network, the bacterial metabolisms predicted from 16S rRNA gene high-throughput sequencing, and the microbiome intact polar lipids were investigated in the BSCs and the underlying sediment deep layers (DLs). Different bacterial microbiomes inhabited the BSCs and the DLs, and their composition varied among sites, indicating a niche-specific role of the micro-environmental conditions in the bacterial communities' assembly. In the heterogeneous sediments of glacier moraines, physico-chemical and micro-climatic variations at the site-spatial scale are crucial in shaping the microbiome microvariability and structuring the pioneer bacterial communities during pedogenesis.

Integrated Omics Reveal Time-Resolved Insights into T4 Phage Infection of E. coli on Proteome and Transcriptome Levels.

Bacteriophages are highly abundant viruses of bacteria. The major role of phages in shaping bacterial communities and their emerging medical potential as antibacterial agents has triggered a rebirth of phage research. To understand the molecular mechanisms by which phages hijack their host, omics technologies can provide novel insights into the organization of transcriptional and translational events occurring during the infection process. In this study, we apply transcriptomics and proteomics to characterize the temporal patterns of transcription and protein synthesis during the T4 phage infection of E. coli. We investigated the stability of E. coli-originated transcripts and proteins in the course of infection, identifying the degradation of E. coli transcripts and the preservation of the host proteome. Moreover, the correlation between the phage transcriptome and proteome reveals specific T4 phage mRNAs and proteins that are temporally decoupled, suggesting post-transcriptional and translational regulation mechanisms. This study provides the first comprehensive insights into the molecular takeover of E. coli by bacteriophage T4. This data set represents a valuable resource for future studies seeking to study molecular and regulatory events during infection. We created a user-friendly online tool, POTATO4, which is available to the scientific community and allows access to gene expression patterns for E. coli and T4 genes.