Community Structure Of Bacteria Research Articles

The Xinjiang Uygur Autonomous Region, situated in northwest China, boasts a unique geographical position and a consequent variety of environmental characteristics. T. truncatus is prevalent throughout this region as the primary pest affecting various crops. In this study, we analyzed the microbial community structures of endosymbiotic bacteria in T. truncatus collected from 17 regions and three host plants in Xinjiang using 16S rRNA sequencing. Through composition analysis of the endosymbiotic bacteria in T. truncatus from Xinjiang, it was found that the dominant bacterial phyla were Pseudomonadota and Bacillota. At the genus level, in addition to Wolbachia, Cardinium, and Spiroplasma (common symbiotic bacteria in T. truncatus), the infection rate of Rickettsia in T. truncatus in Xinjiang was found to be 92.8%. The diversity of the endosymbiotic bacteria community in T. truncatus is shaped by both host plant species and geographical region. Specifically, the endosymbiotic bacterial diversity in T. truncatus populations on corn was significantly higher than that observed in populations on cotton and soybean (p < 0.05). Furthermore, we discovered the diversity of endosymbiotic bacteria in T. truncatus was significantly higher in southern Xinjiang than in northern Xinjiang (p < 0.05).

EpicPCR-based identification of diversity and community structure of environmental alkBs-carrying bacteria.

Heavy metal (HM) contamination of soil is a worldwide problem with adverse consequences for the environment and human health. Microorganisms, as the most active fraction in soil, play a pivotal role in assessing changes in soil quality and maintaining ecological equilibrium. Accordingly, screening efficient microorganisms for remediating contaminated soils has emerged as a key research focus. This study employed high-throughput sequencing and conducted in situ field surveys to investigate the impacts of long-term HM pollution with varying severity on soil physicochemical properties, as well as the community structure and diversity of bacteria and fungi. The results showed that the major soil physiochemical properties and the bacterial and fungal β diversity significantly changed with the increase in HM pollution levels. The relative abundances of Chloroflexi, Myxococcota and Nitrospirota among bacteria, along with Chytridiomycota and Talaromyces among fungi, increased significantly with rising HM pollution levels. In low-, medium- and highly contaminated soils, the dominant bacterial species were OTU10618 (Micrococcales), OTU6447 (Chthoniobacterales), and OTU7447 (Burkholderiales), while the dominant fungal species were OTU3669 (Glomerellales), OTU397 (Olpidiales), and OTU2568 (Mortierellales). Bacterial communities were mainly affected by soil-available phosphorus, available cadmium (Cd) and available Pb, while fungal communities were predominantly influenced by soil-available phosphorus, soil organic carbon and total Pb content. These findings demonstrate that soil microorganisms in chronically HM-contaminated soils exhibit adaptive shifts, and this study thereby provides critical implications for assessing the remediation potential of diverse microbial taxa in HM-polluted soils.

Soil microbiomes have a crucial role in mulberry development; however, the correlation between the mulberry genotype and rhizosphere microenvironment has not been explored. The rhizosphere microbial community structure and function of rizhosphere bacteria and fungi in five mulberry cultivars and their interaction with soil chemical properties and agronomic traits were analyzed using Illumina-based sequencing. We demonstrated that the composition, structure, and assembly processes of rhizosphere bacteria and fungi exhibited significant differences among mulberry cultivars, and their response to soil chemical traits and leaf yield also varies. The correlations in the bacterial communities were more complex than in the fungal communities among the five cultivars. During the assembly process, bacteria were more stable than fungi. Penicillium and Phytophthora showed a positive correlation with leaf yield and were significantly enriched in the Canghai 12 rhizosphere soil, which exhibited the highest leaf production. Bacillus was a bacterium that showed a significant positive correlation with leaf yield. The saprotrophs exhibited the largest guild in terms of operational taxonomic unit richness. This research indicated that the mulberry genotype is one of the dominant factors in rhizosphere microorganism recruitment and assembly. These findings provide new insights into the complex microbial community soil–plant interaction and probiotic screening.

Studies in environmental bacterial communities are updating our view of the powerful small-scale environmental pressures governing the bacterial community assembly. However, it remains unclear about the processes acting at broader scales, such as the thousand-kilometer scale and highly connected marine habitats. We employed a high-coverage sampling strategy combined with 16S rRNA gene sequencing to investigate the biogeography, assembly mechanisms, and co-occurrence relationships of bacterial communities in the surface waters from the intensively human-affected coasts to the open ocean of the South China Sea. Results revealed a clear geographical clustering of both environmental factors and bacterial communities from a semi-enclosed bay of the Beibu Gulf (BG), a coastal sea area of the Guangdong coast (GD), and an open region of the western South China Sea (WS). Determinant environmental drivers of bacterial communities in the three regions were also distinct: dissolved nutrients in GD, SiO32--Si and Chl a in BG, and temperature and Chl a in WS. The spatial and shared variations of environmental and spatial factors explained the bacterial beta-diversity dominantly. The assembly of bacterial communities was dominated by deterministic processes, particularly homogeneous selection in all regions, but showed significant regional variations in stochastic processes. Key discriminant subcommunities Pseudomonadota and Bacteroidota were assembled by notably high stochastic processes, possibly contributing to the varied bacterial assembly process. Network analysis demonstrated distinctly different co-occurrence patterns among the three regions. Our results highlight the role of spatial features associated with human activity in structuring environmental factors and then driving bacterial distribution patterns in the South China Sea.IMPORTANCECurrent research on the assembly processes of environmental bacterial communities at broader scales, such as the thousand-kilometer scale and highly connected marine habitats, remains limited. The South China Sea is the largest marginal sea in the western Pacific Ocean, exhibiting significant spatial heterogeneity across broader scales from densely human-activity coastal areas to the open ocean. Our findings reveal that the assembly mechanisms of bacterial communities along the thousand-kilometer scale from the coastal areas of the South China Sea to its western regions are dominated by homogeneous selection. Additionally, we discovered that spatial heterogeneity, by structuring local environmental gradients, plays a leading role in shaping the community structure, distribution patterns, and co-occurrence networks of surface water bacteria in the South China Sea. This study enhances the understanding of assembly mechanisms at broader scales and deepens the comprehension of the impact of spatial heterogeneity on bacterial communities.

Long-term continuous monocropping of faba bean destroys the soil ecological balance and increases the occurrence of Fusarium wilt. This study investigated the effects of nitrogen management on soil quality and Fusarium wilt under 1 and 9 years of monocropping at four nitrogen levels (N0-N3; 0, 45, 90 and 135 kg·hm-2 nitrogen fertilizer, respectively). Compared with 1 year of monocropping, 9 years of monocropping significantly reduced plant growth and promoted the occurrence of Fusarium wilt. Under 9 years of monocropping, N1-N3 significantly increased plant height by 13.53%-34.84% and reduced the disease incidence by 7.21%-12.26% compared with N0, with N2 (90 kg·hm-2) exhibiting the best effect. Compared with N0, N2 reduced soil bulk density by 9.40% and simultaneously enhanced the percentage of soil aggregates with R > 0.25 mm by 17.54%. N2 altered the community structure and composition of soil bacteria and fungi; specifically, it increased the abundance of Arthrobacter while decreasing that of Fusarium and Gibberella. Moreover, N2 contributed to increasing soil urease activity by 40.41%, soil neutral phosphatase activity by 22.59% and soil organic matter by 20.08%. Thus, applying 90 kg·hm-2 nitrogen fertilizer effectively enhances soil quality and mitigates Fusarium wilt under continuous monocropping of faba bean.

Spacial distribution of heavy metal (cadmium, iron, lead, aluminum) and community structure of bacteria from Sendangbiru Beach based on environmental DNA 16S rDNA

Rocky desertification, a common phenomenon in karst ecosystems, significantly impacts soil fertility and vegetation restoration. Therefore, understanding the relationship between nitrogen-fixing bacteria and soil properties under different degrees of rocky desertification is crucial. Our experiment was conducted to investigate the bacterial community structure and the main environmental factors affecting the distribution of the nitrogen-fixing bacteria in the nodules of V. villosa. Based on nifH gene sequence analysis, we found that the community composition of nitrogen-fixing bacteria in the nodules was significantly correlated with the degree of rocky desertification. The soil physicochemical properties affecting community composition were analyzed. The results revealed that: (1) The soil water content, alkali-hydrolyzable nitrogen content, and total nitrogen content in the slight rocky desertification area GJ4 were significantly higher than those in the moderate rocky desertification areas KY and MZ3. (2) There were significant differences in the community composition of nitrogen-fixing bacteria across the four rocky desertification areas (R2 = 0.448, P = 0.001). Within the same area, the Shannon index in slight rocky desertification was significantly higher than that of moderate rocky desertification. Rhizobium was the dominant genus. (3) In Gejiu, Yunnan Province, it has been observed that there is a clear negative correlation was observed among rocky desertification grade, soil water content, and nitrogen-fixing bacterial diversity in the typical karst ecosystem. Specifically, intensifying rocky desertification significantly reduces soil moisture and bacterial diversity. The degree of soil rocky desertification, total nitrogen content, total phosphorus content, and pH of soil are the main factors that play a key role in the community composition of the nitrogen-fixing bacteria in the nodules of V. villosa. This study provides a theoretical basis for the control of rocky desertification.

Snails at hydrothermal vents rely on symbiotic bacteria for nutrition; however, the specifics of these associations in adapting to such extreme environments remain underexplored. This study investigated the community structure and metabolic potential of bacteria associated with two Indian Ocean vent snails, Chrysomallon squamiferum and Gigantopelta aegis. Using microscopic, phylogenetic, and metagenomic analyses, this study examines bacterial communities inhabiting the foot and gland tissues of these snails. G. aegis exhibited exceptionally low bacterial diversity (Shannon index 0.14-0.18), primarily Gammaproteobacteria (99.9%), including chemosynthetic sulfur-oxidizing Chromatiales using Calvin-Benson-Bassham cycle and methane-oxidizing Methylococcales in the glands. C. squamiferum hosted significantly more diverse symbionts (Shannon indices 1.32-4.60). Its black variety scales were dominated by Campylobacterota (67.01-80.98%), such as Sulfurovum, which perform sulfur/hydrogen oxidation via the reductive tricarboxylic acid cycle, with both Campylobacterota and Gammaproteobacteria prevalent in the glands. The white-scaled variety of C. squamiferum had less Campylobacterota but a higher diversity of heterotrophic bacteria, including Delta-/Alpha-Proteobacteria, Bacteroidetes, and Firmicutes (classified as Desulfobacterota, Pseudomomonadota, Bacteroidota, and Bacillota in GTDB taxonomy). In C. squamiferum, Gammaproteobacteria, including Chromatiales, Thiotrichales, and a novel order "Endothiobacterales," were chemosynthetic, capable of oxidizing sulfur, hydrogen, or iron, and utilizing the Calvin-Benson-Bassham cycle for carbon fixation. Heterotrophic Delta- and Alpha-Proteobacteria, Bacteroidetes, and Firmicutes potentially utilize organic matter from protein, starch, collagen, amino acids, thereby contributing to the holobiont community and host nutrition accessibility. The results indicate that host species and intra-species variation, rather than the immediate habitat, might shape the symbiotic microbial communities, crucial for the snails' adaptation to vent ecosystems.

Cadmium (Cd) is a highly toxic heavy metal that can greatly affect crops and pose a threat to food security. Plant growth-promoting rhizobacteria (PGPR) are capable of alleviating the harm of Cd to crops. In this research, a Cd-tolerant PGPR strain was isolated and screened from the root nodules of semi-wild soybeans. The strain was identified as Pseudomonas sp. strain KM25 by 16S rRNA. Strain KM25 has strong Cd tolerance and can produce indole-3-acetic acid (IAA) and siderophores, dissolve organic and inorganic phosphorus, and has 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. Under Cd stress, all growth indicators of soybean seedlings were significantly inhibited. After inoculation with strain KM25, the heavy metal stress of soybeans was effectively alleviated. Compared with the non-inoculated group, its shoot height, shoot and root dry weight, fresh weight, and chlorophyll content were significantly increased. Strain KM25 increased the superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities of soybean seedlings, reduced the malondialdehyde (MDA) content, increased the Cd content in the roots of soybeans, and decreased the Cd content in the shoot parts. In addition, inoculation treatment can affect the community structure of endophytic bacteria in the roots of soybeans under Cd stress, increasing the relative abundance of Proteobacteria, Bacteroidetes, Sphingomonas, Rhizobium, and Pseudomonas. This study demonstrates that strain KM25 is capable of significantly reducing the adverse effects of Cd on soybean plants while enhancing their growth.

BackgroundEndohyphal microbial communities, composed of bacteria and viruses residing within fungal hyphae, play important roles in shaping fungal phenotypes, host interactions, and ecological functions. While endohyphal bacteria have been shown to influence fungal pathogenicity, secondary metabolism, and adaptability, much remains unknown about their diversity and host specificity. Even less is known about endohyphal viruses, whose ecological roles and evolutionary dynamics are poorly understood. This study integrates genomic and transcriptomic approaches to (1) characterize the diversity of endohyphal bacterial and viral communities in fungal endophytes isolated from Fagus grandifolia leaves, and (2) assess potential host specialization through phylogenetic signal analyses.ResultsWe analyzed 19 fungal isolates spanning eight fungal orders (Amphisphaeriales, Botryosphaeriales, Diaporthales, Glomerellales, Mucorales, Pleosporales, Sordariales, and Xylariales). Bacterial communities were highly diverse and showed significant phylogenetic signal, with core taxa—such as Bacillales, Burkholderiales, Enterobacterales, Hyphomicrobiales, and Pseudomonadales—shared across hosts. Several bacterial groups were associated with specific fungal orders, suggesting host specialization: Moraxellales, Sphingomonadales, and Streptosporangiaceae in Amphisphaeriales; Enterobacterales, Hyphomicrobiales, and Micrococcales in Glomerellales; and Cytophagales in Diaporthales. In contrast, viral communities were less diverse and dominated by double-stranded DNA viruses, primarily Bamfordvirae and Heunggongvirae. No core viral taxa were detected in metatranscriptomic data, and only a few reads of double-stranded RNA viruses were found.ConclusionsOverall, our results indicate potential host specialization in bacterial endophytes and limited viral diversity in fungal hosts, with dsDNA viruses dominating the endohyphal virome. These findings provide new insights into the ecological and evolutionary dynamics of fungal-associated microbiota. Future work expanding taxonomic reference databases and exploring the functional roles of these microbial symbionts will be essential to understanding their contributions to fungal biology, host interactions, and broader ecosystem processes.Supplementary InformationThe online version contains supplementary material available at 10.1186/s40793-025-00757-8.

Recently, some regions that originally focused on strong-flavor baijiu production started producing Jiang-flavored baijiu, providing a new perspective for studying the dynamic changes in the microbial community during brewing. This study used second-round fermented grains of Jiang-flavored baijiu from three Guizhou production regions (Renhuai, Duyun, and Bijie). By applying metagenomics technology and various analytical and statistical methods, we analyzed the community structures of bacteria and fungi in fermented grains, their functional genes, and their correlations with environmental factors. We identified 1063 bacterial genera and 411 fungal genera. Although the dominant microbial species were similar across regions, their relative abundances differed significantly. α-diversity analysis showed that grains from the Bijie region had higher species richness and evenness indices, indicating the significant impact of geographical location and the strong-flavor baijiu-brewing background on microbial structure and composition. Analysis of similarity and the Wilcoxon rank-sum test revealed significant differences in the microbial communities of different regions, and we identified genera with large differences in abundance, such as Desmospora and Kroppenstedtia among bacteria, and Pyrenophora and Blyttiomyces among fungi. Based on our Kyoto Encyclopedia of Genes and Genomes (KEGG) database analysis, the Duyun region had a significantly higher abundance of metabolism-related genes at the tertiary KEGG level. Redundancy analysis showed that six environmental factors (relative humidity, daily temperature difference, elevation, annual mean temperature, extreme cold temperature, and annual precipitation) exerted complex effects on microbial functional genes in fermented grains. Carbon metabolism, antibiotic biosynthesis, and elevation were positively correlated with microbial functional genes. Actinobacteria are crucial for carbon metabolism, followed by Proteobacteria and Chloroflexi. This study elucidated the structural and functional characteristics of microbial communities in second-round fermented grains of Jiang-flavored baijiu under production area transitions and proposed policy recommendations to promote the differentiated development of the baijiu industry.

Agricultural soil has become an important reservoir and transmission source of antibiotic resistance genes （ARGs） because of the extensive application of organic fertilizers such as livestock and poultry manure in organic agriculture production. This greatly increases the risk of foodborne transmission of ARGs in organic agricultural products. However， the extent of ARGs contamination in different types of organic vegetables and its driving factors remain unclear. Therefore， two organic and traditional farming species： green radish （Raphanus sativus L.） and coriander （Coriandrum sativum L.） species were selected as representatives to compare and analyze the abundance of ARGs and mobile gene elements （MGEs） and microbial community structure of the vegetable surface bacteria and endophytic bacteria using real-time PCR and 16S rRNA sequencing technology. Compared to conventional farming practices， organic farming significantly increased the abundance of ARGs among both epiphytic and endophytic bacteria on vegetables. The enrichment levels reached up to 78.9 times and 1.99 times， respectively. Furthermore， compared with that in coriander， green radishes exhibited a higher accumulation of ARGs. Similarly， the relative abundance of MGEs in endophytic bacteria of organically grown vegetables was significantly higher than those of the conventionally grown vegetables. Additionally， the abundance of MGEs positively correlated with the abundance of ARGs （P<0.05）， indicating that the organic farming practices increased the abundance of ARGs in the microbiomes of the vegetables by promoting horizontal gene transfer. Furthermore， network analysis showed that the interactions between ARGs and bacteria were more complex under organic farming practices， enriching 30 bacterial genera as potential hosts. Among them， 14 bacterial genera （e.g.， Microbacterium， Aeromicrobium， and Glutamicibacter） were significantly associated with high-risk ARGs （aadA， tetM， and floR）. These findings demonstrated that organic farming practices can increase the risk of human intake of ARGs by introducing potential ARG host bacteria and enriching MGEs， and root vegetables are more significantly affected by organic farming practices compared to leafy vegetables. This study provides a theoretical basis for assessing the health risks of ARGs contamination in edible vegetables under organic agricultural ecosystems.

ABSTRACTSoil microbial biodiversity plays a fundamental role in regulating dryland ecosystem multifunctionality, being influenced by various environmental factors, particularly plant cover and soil properties. However, the complex interactions among soil microbial communities, plant communities, and soil physicochemical properties in desert steppe ecosystems remain inadequately understood. To address this knowledge gap, we examined the relationships between aboveground plant communities and soil environmental parameters (including nitrate nitrogen, pH, cation exchange capacity, and effective phosphorus) and their influence on the diversity and community structure of soil bacteria, archaea, and fungi across 37 desert steppe sites in Bayannur, Inner Mongolia, a typical northern China's dryland region. Our results showed that bacterial diversity exhibited significant variation among plant communities, with notably higher diversity in Stipa breviflora‐dominated soils compared to Peganum harmala‐dominated soils. The microbial communities were characterized by dominant phyla: Acidobacteriota (21.5%) in bacteria, Crenarchaeota (97.3%) in archaea, and Ascomycota (82.1%) in fungi. Bacterial diversity was significantly correlated with soil pH, available potassium, and carbonate content, while archaeal diversity showed strong correlations with ammonium nitrogen, available phosphorus, carbonate content, and cation exchange capacity. Fungal diversity, however, exhibited significant correlation only with available phosphorus. Environmental factors explained varying degrees of community structure variations, with the highest explanatory power for archaea (66.1%), followed by bacteria (49.0%) and fungi (32.8%). Structural equation modeling (SEM) revealed that plant communities influenced bacterial communities primarily through modifications in soil pH and ion contents. These findings underscore the critical role of plant communities and soil properties in shaping soil microbial diversity patterns. Given the essential function of biodiversity in ecosystem processes, our findings propose that soil bacterial diversity that was sensitive to vegetation shifts and closely linked to soil nutrient dynamics serves as a valuable bioindicator for monitoring and assessing degradation in desert steppe ecosystems.

Evidence from an increasing number of studies indicates that plant endophytic microorganisms play a significant role during biotic and abiotic stress resistance. To date, however, only a handful of studies on endophytes in response to the presence of phytoplasmas have been conducted. The production of jujube (Ziziphus jujuba) is threatened by jujube witches’ broom (JWB) disease, which is associated with the presence of the JWB phytoplasma ‘Candidatus Phytoplasma ziziphi’. To investigate the impact of jujube witches’ broom phytoplasma on the endophyte populations in jujube, high-throughput sequencing was performed in healthy and JWB-infected orchard jujube trees and in vitro jujube shoots. The results showed that the presence of JWB phytoplasma in jujube altered the abundance, diversity, and community structure of endophytic bacteria and fungi. In the branches and the roots, the presence of JWB phytoplasma was associated with an increase in the richness of the endophytic communities and a decrease in their diversity, with the phyla Proteobacteria, Firmicutes, and Bacteroidota and the genus ‘Ca. Phytoplasma’ becoming the most abundant. The presence of phytoplasmas was also associated with the remodeling of the endophytic microorganisms’ interaction network, shifting to a simpler biodiversity state. These results demonstrate the response of the jujube endophytic community to the presence of JWB phytoplasmas and shed light on the possible antagonistic agents that could be further evaluated for JWB disease biocontrol.

Modern sustainable agriculture often relies on pesticide application, which may unintentionally affect non-target soil microorganisms. This study assessed the effects of commonly used pesticides in cabbage cultivation on bacteria diversity, composition, and abundance in soils from some farming communities in Bosome Freho District, Ghana. The pesticides included a neonicotinoid (acetamiprid), microbial agents (Pieris rapae granulosis virus+ Bacillus thuringiensis), avermectin (emamectin benzoate), and pyrrole (chlorfenapyr). Soil samples were collected from non-contaminated (NCS), abandoned pesticide-contaminated (AB-PCS) and actively pesticide-contaminated (AC-PCS) soils. Bacteria communities were analysed in the soil at phylum, class, order, family, genus, and species levels using 16S rRNA gene sequencing. The soils were also analyzed for physicochemical properties. Our results showed a decrease in bacteria diversity and abundance in pesticide-contaminated soils in the following order: NCS > AB-PCS > AC-PCS. Sorensen’s coefficient of similarity indicated major shifts in bacteria taxa composition due to pesticide contamination. In NCS, Pseudomonas veronii, Bacillus sp., and Prevotella albensis were the most abundant species, while Rhodoplanes elegans and Nostocoida limicola dominated AB-PCS. In AC-PCS, R. elegans, Gemmata obscuriglobus, Nitrospira calida, and N. limicola were the most abundant species. The abundance of Bacillus sp., P. veronii, and P. albensis decreased in the contaminated soils, while the abundance of N. calida, Cystobacter sp., Pedomicrobium australicum and Byssovorax cruenta was higher in the contaminated soils. Key genera involved in nutrient cycling such as Clostridium, Bacillus, Prevotella, Pseudomonas, and Arthrobacter, declined in abundance in pesticide exposed soils. In contrast, an increase in abundance of various taxa such as Pedomicrobium, Hyphomicrobiaceae, Pirellulaceae, Comamonadaceae, Nitrospirales, Nitrospira, Anaerolineae, Planctomycetes, Acidobacteriaí and Nitrospirae was observed in the contaminated soils. These bacteria may possess bioremediation potential that could be exploited for environmental remediation. Soil physicochemical properties and nutrient levels varied across the three soil treatments, with potential implications for bacteria community structure.

Biological soil crusts (referred to as biocrusts) constitute prominent components within the ecosystem of tropical coral islands in the South China Sea, covering approximately 6.25% of the island’s terrestrial surface. Biocrusts are the key to the restoration of the island ecosystem. It is widely acknowledged that phototrophic microorganisms profoundly contribute to biocrust formation and development. They provide fixed carbon and nitrogen and produce exopolysaccharides for the BSC ecosystems. Although aerobic anoxygenic phototrophic bacteria (AAPB) are an important functional group of phototrophic microorganisms, the community characteristics of AAPB in coral island biocrusts and their role in the formation of biocrusts have rarely been reported. In this study, we employed amplifications of the pufM gene to characterize the AAPB communities of biocrusts on a tropical coral island. The outcomes revealed a discernible augmentation in both the abundance and richness of AAPB concurrent with the formation of biocrusts, concomitantly with a decrement in diversity. Within the AAPB communities, the Pseudomonadota (Proteobacteria) phylum emerges as the prevailing dominion, indicating marked differentiations in terms of family and genus compositions between the biocrust and bare soil. Canonical correlation analysis has unveiled a robust and meaningful correlation between the AAPB composition and the attributes of the soil, including total nitrogen, total organic carbon, total phosphorus, pH, and calcium content. Furthermore, co-occurrence network patterns shift with biocrust formation, enhancing stability. Meanwhile, keystone taxa analysis revealed specific OTUs associated with each soil type, with genus Brevundimonas as the main group. Furthermore, pure-culture AAPB strains isolated from biocrusts exhibited a panorama of diversity, predominantly belonging to Pseudomonadota. Particularly, the Skermanella and Erythrobacter genera demonstrated strong exopolysaccharide secretion and sand-binding capabilities. This study sheds light on the significant functional role of AAPB in tropical coral island biocrusts, expanding our understanding of their contribution to ecosystem services, and providing valuable insights for ecological restoration efforts on coral islands.

The long-term post-fire recovery phase is a critical stage for forest ecosystems to progress toward regeneration and mature succession. During this process, soil bacteria exhibit greater environmental adaptability, rapidly driving nutrient cycling and facilitating vegetation restoration. This study investigated the community structure and diversity of soil bacteria during long-term recovery after forest fires in the cold temperate zone, focusing on soils from the 2000 fires in Daxing’anling. Soil samples were classified into Low (L), Moderate (M), and High (H) fire damage intensity, with bacterial community composition and diversity analyzed using Illumina sequencing technology. After long-term fire recovery, the contents of soil organic carbon, black carbon, total nitrogen, alkaline nitrogen, available phosphorus, and available potassium were significantly higher elevated (p < 0.05), and water content was significantly lower, compared with that in the control check (CK) group. Soil urease, fluorescein diacetate, soil acid phosphatase, and soil dehydrogenase activities were significantly higher, and soil sucrase activity was significantly lower in H. There was a significant difference in the Alpha diversity index among the groups. Compared with CK, the Shannon index was significantly increased (p < 0.05) in L, while both Chao1 and Shannon indices were significantly decreased (p < 0.05) in M and significantly higher in H than CK. The results of the PCoA showed that there was a significant difference in the Beta diversity of the bacterial community among the groups (R2 = 0.60 p = 0.001). The dominant bacteria groups were Proteobacteria and Acidobacteriota, while Actinobacteria became the new dominant group during the long-term post-fire recovery. AP, WC, DOC, MBC, S-DHA, and S-SC were significantly and positively correlated with soil bacterial diversity (p < 0.05). The results of the co-occurrence network analysis showed that all groups were dominated by symbiotic relationships, with M having the highest network complexity and strongest competitive effects. This study found that the physicochemical properties of soils recovered over a long period of time after fire returned to or exceeded the unfired forest condition. The Actinobacteria phylum became a new dominant bacterial group, with stronger network complexity and competition, in the process of forest recovery after moderate fire.

Emerging observational studies suggest air pollution can influence the gut microbiome. However, this association is often highly confounded by factors such as diet and poverty. The gut virome may influence respiratory health independent of the gut microbiome. We recently demonstrated in a randomized waitlist-controlled trial (ClinicalTrials.gov NCT03351504) that a clean lighting intervention reduced personal exposure to air pollution among adult women in rural Uganda. To determine the effect of a solar lighting intervention on changes to the gut microbiome and virome and secondarily to determine association between these changes on lung health. Between 2018 and 2019, we collected stool samples and assessed respiratory symptoms and spirometry from 80 adult women living in rural Uganda at baseline, 12 and 18 months post-randomization. The intervention group received a solar lighting system after randomization, while the waitlist-controlled group received one at 12 months. Deep metagenomics sequencing of stool was performed and profiled for non-viral and viral taxonomic composition. The primary analysis focused on pre- vs. post-intervention changes due power considerations, adjusting for potential confounding by age, diet, antibiotic use, and season. A sensitivity analysis was conducted using intention-to-treat principles. When comparing pre- vs. post-intervention periods, we used sparse partial least squares models to identify non-viral and viral signatures of reduced air pollution exposure. Mixed effects models were used to evaluate changes in health outcomes as well as associations between microbial signatures of reduced air pollution exposure and health. The average age was 39.2 years. The solar lighting intervention led to larger changes in viral compared to non-viral microbial community structure and differential abundance of bacteria, eukaryotes, and viruses. Provision of solar lighting systems was associated with a reduction in the presence of respiratory symptoms from 57.1% to 36.1% (p = 0.002) while there was no impact on lung function. Microbiome and virome signatures had AUCs of 0.74 and 0.76 respectively, in predicting pre- vs. post-intervention stool samples. Microbiome signatures were associated with a lower risk of respiratory symptoms (OR 0.68 (0.49-0.94), p = 0.020). Among adult women living in rural Uganda, both non-viral and viral components of the gut microbial community changed after a clean lighting intervention. Microbiome signatures reflective of lower air pollution exposures were associated with improved respiratory symptoms. These observations suggest that air pollution may influence lung health through the gut-lung axis, warranting further exploration in future intervention studies. https://doi.org/10.1289/EHP16002.

Abstract. While the sources of dissolved organic matter (DOM) in the open ocean are relatively well identified, its fate due to microbial activity is still evolving. Here, we explored how microbial community structure, growth, and grazing of phytoplankton and heterotrophic bacteria influenced the DOM pool and the transformation of its fluorescent fraction. Dilution experiments were performed during the productive season on the Patagonian Shelf (SW Atlantic Ocean), a region of intense biological activity, with peak productivity observed at the shelf break front. Although phytoplankton biomass was higher than that of bacteria, protists selectively preyed on the faster-growing bacterial population, denoting trophic specificity of grazers. High trophic coupling was suggested by the biomass distribution of protistan consumers and their prey, which predominantly exhibited an inverted trophic pyramid structure. An exception to this pattern was observed at the highly productive shelf break front, where a traditional bottom-heavy pyramid emerged, indicating that most phytoplankton evaded protist predation despite evidence of herbivory. Bacterial consumption of DOM appeared uncoupled from its total amount but was influenced by DOM complexity, while the bacterial production of humic-like substances from protistan plankton precursors observed in most experiments highlighted a potential pathway for carbon sequestration. Protistan grazers also significantly influenced DOM dynamics by scaling their DOM contribution in response to the intensity of grazing on heterotrophic bacteria, regardless of productivity levels. This effect likely arises from reducing the number of active DOM-consuming bacteria and by providing egestion DOM compounds. At the onset of the productive season, high bacterial growth rates stimulate protistan grazing, which serves as a link between bacterial biomass and higher trophic levels. However, as grazing pressure increases, protists can also contribute to the accumulation of a fraction of DOM.