Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle.

The body-wide human microbiome plays a role in health, but its full diversity remains uncharacterized, particularly outside of the gut and in international populations. We leveraged 9,428 metagenomes to reconstruct 154,723 microbial genomes (45% of high quality) spanning body sites, ages, countries, and lifestyles. We recapitulated 4,930 species-level genome bins (SGBs), 77% without genomes in public repositories (unknown SGBs [uSGBs]). uSGBs are prevalent (in 93% of well-assembled samples), expand underrepresented phyla, and are enriched in non-Westernized populations (40% of the total SGBs). We annotated 2.85 M genes in SGBs, many associated with conditions including infant development (94,000) or Westernization (106,000). SGBs and uSGBs permit deeper microbiome analyses and increase the average mappability of metagenomic reads from 67.76% to 87.51% in the gut (median 94.26%) and 65.14% to 82.34% in the mouth. We thus identify thousands of microbial genomes from yet-to-be-named species, expand the pangenomes of human-associated microbes, and allow better exploitation of metagenomic technologies.

Deforestation impacts soil biodiversity and ecosystem services worldwide.

Deforestation poses a global threat to biodiversity and its capacity to deliver ecosystem services. Yet, the impacts of deforestation on soil biodiversity and its associated ecosystem services remain virtually unknown. We generated a global dataset including 696 paired-site observations to investigate how native forest conversion to other land uses affects soil properties, biodiversity, and functions associated with the delivery of multiple ecosystem services. The conversion of native forests to plantations, grasslands, and croplands resulted in higher bacterial diversity and more homogeneous fungal communities dominated by pathogens and with a lower abundance of symbionts. Such conversions also resulted in significant reductions in carbon storage, nutrient cycling, and soil functional rates related to organic matter decomposition. Responses of the microbial community to deforestation, including bacterial and fungal diversity and fungal guilds, were predominantly regulated by changes in soil pH and total phosphorus. Moreover, we found that soil fungal diversity and functioning in warmer and wetter native forests is especially vulnerable to deforestation. Our work highlights that the loss of native forests to managed ecosystems poses a major global threat to the biodiversity and functioning of soils and their capacity to deliver ecosystem services.

Expanding Archaeal Diversity and Phylogeny: Past, Present, and Future.

The discovery of the Archaea is a major scientific hallmark of the twentieth century. Since then, important features of their cell biology, physiology, ecology, and diversity have been revealed. Over the course of some 40 years, the diversity of known archaea has expanded from 2 to about 30 phyla comprising over 20,000 species. Most of this archaeal diversity has been revealed by environmental 16S rRNA gene amplicon sequencing surveys using a broad range of universal and targeted primers. Of the few primers that target a large fraction of known archaeal diversity, all display a bias against recently discovered lineages, which limits studies aiming to survey overall archaeal diversity. Induced by genomic exploration of archaeal diversity, and improved phylogenomics approaches, archaeal taxonomic classification has been frequently revised. Due to computational limitations and continued discovery of new lineages, a stable archaeal phylogeny is not yet within reach. Obtaining phylogenetic and taxonomic consensus of archaea should be a high priority for the archaeal research community.

Coordinated elimination of bacterial taxa optimally attenuates alloimmunity and prolongs allograft survival.

This study aimed to dissect the relationship between specific gut commensal bacterial subgroups, their functional metabolic pathways, and their impact on skin allograft outcome and alloimmunity. We previously showed that oral broad-spectrum antibiotic (Abx) pretreatment in mice delayed skin, heart, and lung allograft rejection and dampened alloimmune responses. Here, rationally designed Abx combinations targeting major bacterial groups were used to elucidate their individual contribution to modulating alloimmune responses. Abx cocktails targeting intestinal gram-negative, gram-positive, or anaerobic/gram-positive bacteria by oral gavage, all delayed skin allograft rejection, and reduced alloreactive T cell priming to different extents. Notably, the most pronounced extension of skin allograft survival and attenuation of alloimmunity were achieved when all gut bacterial groups were simultaneously targeted. These results suggest a model in which the strength of the alloimmune response is additively tuned up by gut microbial diversity. Shotgun metagenomic sequencing enabled strain-level resolution and identified a shared commensal, Parabacteroides distasonis, as the most enriched following all Abx treatments. Oral administration of P.distasonis to mice harboring a diverse microbiota significantly prolonged skin allograft survival, identifying a probiotic with therapeutic benefit in transplantation.

Microbiome composition recovery after liver transplantation correlates with initial liver disease severity and antibiotics treatment.

Liver transplantation (LT) is crucial for end-stage liver disease, but it is linked to infection risks. Pathobionts, microorganisms potentially harmful under specific conditions, can cause complications posttransplant. Monitoring such pathogens in fecal samples can be challenging and therefore remains underexplored post-LT. This study aimed to analyze the gut microbiome before and after LT, tracking pathobionts and correlating clinical data. The study involved 17 liver transplant recipients, 17 healthy relatives (spouses), and 13 donors. Gut samples collected pretranplantation and posttransplantation underwent bacterial and fungal profiling through DNA sequencing. Quantitative polymerase chain reaction was used to assess microbial load. Statistical analyses included alpha and beta diversity measures, differential abundance analysis, and correlation tests between microbiome and clinical parameters. Microbiome analysis revealed dynamic changes in diversity posttransplant. Notably, high-severity patients showed persistent and greater dysbiosis during the first months post-LT compared with low-severity patients, partly due to an antibiotic treatment pre-LT. The analysis identified a higher proportion of pathogens such as Escherichia coli/Shigella flexneri in high-severity cases posttransplant. Furthermore, butyrate producers including Roseburia intestinalis, Anaerostipes hadrus, and Eubacterium coprostanoligenes were positively correlated with levels of albumin. This study offers valuable insights into post-LT microbiome changes, shedding light on the need for tailored prophylactic treatment post-LT.

Enterobacter ludwigii b3 in the rhizosphere of wild rice assists cultivated rice in mitigating drought stress by direct and indirect methods.

Drought is the primary factor limiting rice production in ecosystems. Wild rice rhizosphere bacteria possess the potential to assist in the stress resistance of cultivated rice. This study examines the impact of wild rice rhizosphere bacteria on cultivated rice under drought conditions. From the rhizosphere soil of wild rice, 20 potential drought-resistant strains were isolated. Subsequent to the screening, the most effective strain b3, was identified as Enterobacter ludwigii. Pot experiments were conducted on the cultivated Changbai 9 rice. It was found that inoculation with the E. ludwigii b3 strain improved the drought resistance of the rice, promotion of rice growth (shoot height increased by 13.47 %), increased chlorophyll content (chlorophyll a, chlorophyll b and carotenoid increased by 168.74 %, 130.68 % and 87.89 %), improved antioxidant system (content of glutathione was increased by 60.35 %), and accumulation of osmotic regulation substances (soluble sugar and soluble protein increased by 70.36 % and 142.03 %). Furthermore, E. ludwigii b3 had a transformative effect on the rhizosphere bacterial community of cultivated rice, increasing its abundance and diversity while simultaneously recruiting beneficial rhizosphere bacteria, resulting in a more complex community. Additionally, E. ludwigii b3 acted directly and indirectly on cultivated rice through its metabolites (organic acids, amino acids, flavonoids and other substances), which helped alleviate drought stress. In conclusion, the E. ludwigii b3 shows promise as a drought-resistant strain and has the potential to improve the growth and productivity of cultivated rice in arid agricultural ecosystems. This study represents the first investigation of E. ludwigii in the rhizosphere of wild rice under drought conditions on cultivated rice.

Soil fungal community structure and function response to rhizoma perennial peanut cultivars.

BACKGROUND: Crop-associated microorganisms play a crucial role in soil nutrient cycling, and crop growth, and health. Fine-scale patterns in soil microbial community diversity and composition are commonly regulated by plant species or genotype. Despite extensive reports in different crop or its cultivar effects on the microbial community, it is uncertain how rhizoma peanut (RP, Arachis glabrata Benth.), a perennial warm-season legume forage that is well-adapted in the southern USA, affects soil microbial community across different cultivars. RESULTS: This study explored the influence of seven different RP cultivars on the taxonomic composition, diversity, and functional groups of soil fungal communities through a field trial in Marianna, Florida, Southern USA, using next-generation sequencing technique. Our results showed that the taxonomic diversity and composition of the fungal community differed significantly across RP cultivars. Alpha diversity (Shannon, Simpson, and Pielou's evenness) was significantly higher in Ecoturf but lower in UF_Peace and Florigraze compared to other cultivars (p < 0.001). Phylogenetic diversity (Faith's PD) was lowest in Latitude compared to other cultivars (p < 0.0001). The dominant phyla were Ascomycota (13.34%), Mortierellomycota (3.82%), and Basidiomycota (2.99%), which were significantly greater in Florigraze, UF_Peace, and Ecoturf, respectively. The relative abundance of Neocosmospora was markedly high (21.45%) in UF_Tito and showed large variations across cultivars. The relative abundance of the dominant genera was significantly greater in Arbrook than in other cultivars. There were also significant differences in the co-occurrence network, showing different keystone taxa and more positive correlations than the negative correlations across cultivars. FUNGuild analysis showed that the relative abundance of functional guilds including pathogenic, saprotrophic, endophytic, mycorrhizal and parasitic fungi significantly differed among cultivars. Ecoturf had the greatest relative abundance of mycorrhizal fungal group (5.10 ± 0.44), whereas UF_Peace had the greatest relative abundance of endophytic (4.52 ± 0.56) and parasitic fungi (1.67 ± 0.30) compared to other cultivars. CONCLUSIONS: Our findings provide evidence of crop cultivar's effect in shaping fine-scale fungal community patterns in legume-based forage systems.

Difference in microbial community structure along a gradient of crater altitude: insights from the Nushan volcano.

The variation in the soil microbial community along the altitude gradient has been widely documented. However, the structure and function of the microbial communities distributed along the altitude gradient in the crater still need to be determined. We gathered soil specimens from different elevations within the Nushan volcano crater to bridge this knowledge gap. We investigated the microbial communities of bacteria and fungi in the soil. It is noteworthy that the microbial alpha diversity peaks in the middle of the crater. However, network analysis shows that bacterial (nodes 760 vs 613 vs 601) and fungal (nodes 328 vs 224 vs 400) communities are most stable at the bottom and top of the crater, respectively. Furthermore, the soil microbial network exhibited a decline, followed by an increase across varying altitudes. The core microorganisms displayed the highest correlation with pH and alkaline phosphatase (AP, as determined through redundancy analysis (RDA) and Mantel tests for correlation analysis. The fungal community has a higher number of core microorganisms, while the bacterial core microorganisms demonstrate greater susceptibility to environmental factors. In conclusion, we utilized Illumina sequencing techniques to assess the disparities in the structure and function of bacteria and fungi in the soil.IMPORTANCEThese findings serve as a foundation for future investigations on microbial communities present in volcanic soil.

Continuous planting of euhalophyte Suaeda salsa enhances microbial diversity and multifunctionality of saline soil.

Halophyte-based remediation emerges as a novel strategy for ameliorating saline soils, offering a sustainable alternative to conventional leaching methods. While bioremediation is recognized for its ability to energize soil fertility and structure, the complex interplays among plant traits, soil functions, and soil microbial diversity remain greatly unknown. Here, we conducted a 5-year field experiment involving the continuous cultivation of the annual halophyte Suaeda salsa in saline soils to explore soil microbial diversity and their relationships with plant traits and soil functions. Our findings demonstrate that a decline in soil salinity corresponded with increases in the biomass and seed yield of S. salsa, which sustained a consistent seed oil content of approximately 22% across various salinity levels. Significantly, prolonged cultivation of halophytes substantially augmented soil microbial diversity, particularly from the third year of cultivation. Moreover, we identified positive associations between soil multifunctionality, seed yield, and taxonomic richness within a pivotal microbial network module. Soils enriched with taxa from this module showed enhanced multifunctionality and greater seed yields, correlating with the presence of functional genes implicated in nitrogen fixation and nitrification. Genomic analysis suggests that these taxa have elevated gene copy numbers of crucial functional genes related to nutrient cycling. Overall, our study emphasizes that the continuous cultivation of S. salsa enhances soil microbial diversity and recovers soil multifunctionality, expanding the understanding of plant-soil-microbe feedback in bioremediation.IMPORTANCEThe restoration of saline soils utilizing euhalophytes offers a viable alternative to conventional irrigation techniques for salt abatement and soil quality enhancement. The ongoing cultivation of the annual Suaeda salsa and its associated plant traits, soil microbial diversity, and functionalities are, however, largely underexplored. Our investigation sheds light on these dynamics, revealing that cultivation of S. salsa sustains robust plant productivity while fostering soil microbial diversity and multifunctionality. Notably, the links between enhanced soil multifunctionality, increased seed yield, and network-dependent taxa were found, emphasizing the importance of key microbial taxa linked with functional genes vital to nitrogen fixation and nitrification. These findings introduce a novel understanding of the role of soil microbes in bioremediation and advance our knowledge of the ecological processes that are vital for the rehabilitation of saline environments.

Soil microbial subcommunity assembly mechanisms are highly variable and intimately linked to their ecological and functional traits.

Revealing the mechanisms underlying soil microbial community assembly is a fundamental objective in molecular ecology. However, despite increasing body of research on overall microbial community assembly mechanisms, our understanding of subcommunity assembly mechanisms for different prokaryotic and fungal taxa remains limited. Here, soils were collected from more than 100 sites across southwestern China. Based on amplicon high-throughput sequencing and iCAMP analysis, we determined the subcommunity assembly mechanisms for various microbial taxa. The results showed that dispersal limitation and homogenous selection were the primary drivers of soil microbial community assembly in this region. However, the subcommunity assembly mechanisms of different soil microbial taxa were highly variable. For instance, the contribution of homogenous selection to Crenarchaeota subcommunity assembly was 70%, but it was only around 10% for the subcommunity assembly of Actinomycetes, Gemmatimonadetes and Planctomycetes. The assembly of subcommunities including microbial taxa with higher occurrence frequencies, average relative abundance and network degrees, as well as wider niches tended to be more influenced by homogenizing dispersal and drift, but less affected by heterogeneous selection and dispersal limitation. The subcommunity assembly mechanisms also varied substantially among different functional guilds. Notably, the subcommunity assembly of diazotrophs, nitrifiers, saprotrophs and some pathogens were predominantly controlled by homogenous selection, while that of denitrifiers and fungal pathogens were mainly affected by stochastic processes such as drift. These findings provide novel insights into understanding soil microbial diversity maintenance mechanisms, and the analysis pipeline holds significant value for future research.

Soil selenium enhanced the resistance of oilseed rape to Sclerotinia sclerotiorum by optimizing the plant microbiome.

Plant can recruit beneficial microbes to enhance their ability to resist disease. Selenium is well established as a beneficial element in plant growth, but its role in mediating microbial disease resistance remained poorly understood. Here, we investigated the correlation between selenium, oilseed rape rhizosphere microbes and Sclerotinia sclerotiorum. Soil application of 0.5 and 1.0 mg/kg selenium significantly increased the resistance of oilseed rape to Sclerotinia sclerotiorum compared with no selenium application, and the disease inhibition rate was higher than 20%. The disease resistance of oilseed rape was related to rhizosphere microorganisms, and beneficial bacteria isolated from the rhizosphere inhibited Sclerotinia stem rot. Burkholderia cepacia, and synthetic community enhanced plant disease resistance through transcriptional regulation and activated plant-induced systemic resistance to protect plants. Besides, inoculation of isolated bacteria optimized the bacterial community structure of leaves and enriched beneficial microorganisms such as Bacillus, Pseudomonas and Sphingomonas. Bacillus isolated from the leaves were sprayed on the detached leaves, and it also performed a significant inhibition effect on Sclerotinia sclerotiorum. Overall, our results suggested that selenium drive plant rhizosphere microorganisms to increase resistance to Sclerotinia sclerotiorum in oilseed rape.

Temperature and CO2 interactively drive shifts in the compositional and functional structure of peatland protist communities.

Microbes affect the global carbon cycle that influences climate change and are in turn influenced by environmental change. Here, we use data from a long-term whole-ecosystem warming experiment at a boreal peatland to answer how temperature and CO2 jointly influence communities of abundant, diverse, yet poorly understood, non-fungi microbial Eukaryotes (protists). These microbes influence ecosystem function directly through photosynthesis and respiration, and indirectly, through predation on decomposers (bacteria and fungi). Using a combination of high-throughput fluid imaging and 18S amplicon sequencing, we report large climate-induced, community-wide shifts in the community functional composition of these microbes (size, shape, and metabolism) that could alter overall function in peatlands. Importantly, we demonstrate a taxonomic convergence but a functional divergence in response to warming and elevated CO2 with most environmental responses being contingent on organismal size: warming effects on functional composition are reversed by elevated CO2 and amplified in larger microbes but not smaller ones. These findings show how the interactive effects of warming and rising CO2 levels could alter the structure and function of peatland microbial food webs-a fragile ecosystem that stores upwards of 25% of all terrestrial carbon and is increasingly threatened by human exploitation.

Canopy nitrogen deposition enhances soil ecosystem multifunctionality in a temperate forest.

Nitrogen (N) deposition affects ecosystem functions crucial to human health and well-being. However, the consequences of this scenario for soil ecosystem multifunctionality (SMF) in forests are poorly understood. Here, we conducted a long-term field experiment in a temperate forest in China, where N deposition was simulated by adding N above and under the canopies. We discover that canopy N addition promotes SMF expression, whereas understory N addition suppresses it. SMF was regulated by fungal diversity in canopy N addition treatments, which is largely due to the strong resistance to soil acidification and efficient resource utilization characteristics of fungi. While in understory N addition treatments, SMF is regulated by bacterial diversity, which is mainly because of the strong resilience to disturbances and fast turnover of bacteria. Furthermore, rare microbial taxa may play a more important role in the maintenance of the SMF. This study provides the first evidence that N deposition enhanced SMF in temperate forests and enriches the knowledge on enhanced N deposition affecting forest ecosystems. Given the divergent results from two N addition approaches, an innovative perspective of canopy N addition on soil microbial diversity-multifunctionality relationships is crucial to policy-making for the conservation of soil microbial diversity and sustainable ecosystem management under enhanced N deposition. In future research, the consideration of canopy N processes is essential for more realistic assessments of the effects of atmospheric N deposition in forests.

Chemotherapy-induced gut microbiome disruption, inflammation, and cognitive decline in female patients with breast cancer.

Chemotherapy is notorious for causing behavioral side effects (e.g., cognitive decline). Notably, the gut microbiome has recently been reported to communicate with the brain to affect behavior, including cognition. Thus, the aim of this clinical longitudinal observational study was to determine whether chemotherapy-induced disruption of the gut microbial community structure relates to cognitive decline and circulating inflammatory signals. Fecal samples, blood, and cognitive measures were collected from 77 patients with breast cancer before, during, and after chemotherapy. Chemotherapy altered the gut microbiome community structure and increased circulating TNF-α. Both the chemotherapy-induced changes in microbial relative abundance and decreased microbial diversity were related to elevated circulating pro-inflammatory cytokines TNF-α and IL-6. Participants reported subjective cognitive decline during chemotherapy, which was not related to changes in the gut microbiome or inflammatory markers. In contrast, a decrease in overall objective cognition was related to a decrease in microbial diversity, independent of circulating cytokines. Stratification of subjects, via a reliable change index based on 4 objective cognitive tests, identified objective cognitive decline in 35% of the subjects. Based on a differential microbial abundance analysis, those characterized by cognitive decline had unique taxonomic shifts (Faecalibacterium, Bacteroides, Fusicatenibacter, Erysipelotrichaceae UCG-003, and Subdoligranulum) over chemotherapy treatment compared to those without cognitive decline. Taken together, gut microbiome change was associated with cognitive decline during chemotherapy, independent of chemotherapy-induced inflammation. These results suggest that microbiome-related strategies may be useful for predicting and preventing behavioral side effects of chemotherapy.

Effect of nitrogen reduction by chemical fertilization with green manure (Vicia sativa L.) on soil microbial community, nitrogen metabolism and and yield of Uncaria rhynchophylla by metagenomics.

Uncaria rhynchophylla is an important herbal medicine, and the predominant issues affecting its cultivation include a single method of fertilizer application and inappropriate chemical fertilizer application. To reduce the use of inorganic nitrogen fertilization and increase the yield of Uncaria rhynchophylla, field experiments in 2020-2021 were conducted. The experimental treatments included the following categories: S1, no fertilization; S2, application of chemical NPK fertilizer; and S3-S6, application of chemical fertilizers and green manures, featuring nitrogen fertilizers reductions of 0%, 15%, 30%, and 45%, respectively. The results showed that a moderate application of nitrogen fertilizer when combined with green manure, can help alleviate soil acidification and increase urease activity. Specifically, the treatment with green manure provided in a 14.71-66.67% increase in urease activity compared to S2. Metagenomics sequencing results showed a decrease in diversity in S3, S4, S5, and S6 compared to S2, but the application of chemical fertilizer with green manure promoted an increase in the relative abundance of Acidobacteria and Chloroflexi. In addition, the nitrification pathway displayed a progressive augmentation in tandem with the reduction in nitrogen fertilizer and application of green manure, reaching its zenith at S5. Conversely, other nitrogen metabolism pathways showed a decline in correlation with diminishing nitrogen fertilizer dosages. The rest of the treatments showed an increase in yield in comparison to S1, S5 showing significant differences (p < 0.05). In summary, although S2 demonstrate the ability to enhance soil microbial diversity, it is important to consider the long-term ecological impacts, and S5 may be a better choice.

Effect of commutation on pressure drop and microbial diversity in a horizontal biotrickling filter for toluene removal.

A horizontal biotrickling filter (HBTF) was designed to understand the toluene removal process and microbial community structures. The start-up time of the HBTF, immobilized by the dominant fungi was only about 6 days and the toluene removal efficiency was found to be more than 95% when the inlet toluene concentration remained at around 1560.0 mg/m3. In the stable operation stage of the HBTF, based on not greatly reducing the removal efficiency, a simple and convenient periodic commutation was adopted to reduce the pressure drop (△P) and regulate the distribution of microorganisms in the packing area of the HBTF. The △P decreased from about 90 Pa to 10 Pa after the commutation, which indicated its feasibility. The performance of the HBTF was improved by changing the inlet direction of waste gas flow. When the inlet concentration of toluene was about 640 mg/m3, the removal efficiency was nearly 70.0% before commutation and it remained 95.0-98.0% after commutation. Microbial abundance and diversity analysis showed that the corresponding Shannon-Weiner index was 2.73 and 1.84, respectively. The front section of the HBTF, which was exposed to toluene earlier, consistently exhibited higher microbial diversity than that in the back section. Following commutation, microbial diversity decreased in both the front and back sections, with a maximum decline of around 50%. The main fungi treating toluene were Aplanochytrium, Boletellus, and Exophiala.

Diversity, functions, and antibiotic resistance genes of bacteria and fungi are examined in the bamboo plant phyllosphere that serve as food for the giant pandas.

The phyllosphere of bamboo is rich in microorganisms that can disrupt the intestinal microbiota of the giant pandas that consume them, potentially leading to their death. In the present study, the abundance, diversity, biological functions (e.g., KEGG and CAZyme), and antibiotic resistance genes (ARGs) of bacteria and fungi in two bamboo species phyllosphere (Chimonobambusa szechuanensis, CS; Bashania fangiana, BF) in Daxiangling Nature Reserve (an important part of the Giant Panda National Park) were investigated respectively by amplicon sequencing of the whole 16S rRNA and ITS1-ITS2 genes on PacBio Sequel and whole-metagenome shotgun sequencing on Illumina NovaSeq 6000 platform. The results suggested that there were respectively 18 bacterial and 34 fungi biomarkers between the phyllosphere of the two species of bamboo. Beta diversity of bacteria and fungi communities exited between the two bamboos according to the (un)weighted UniFrac distance matrix. Moreover, the functional analysis showed that the largest relative abundance was found in the genes related to metabolism and global and overview maps. Glycoside hydrolases (GHs) and glycosyl transferases (GTs) have a higher abundance in two bamboo phyllospheres. Co-occurrence network modeling suggested that bacteria and fungi communities in CS phyllosphere employed a much more complex metabolic network than that in BF, and the abundance of multidrug, tetracycline, and glycopeptide resistance genes was higher and closely correlated with other ARGs. This study references the basis for protecting bamboo resources foraged by wild giant pandas and predicts the risk of antibiotic resistance in bamboo phyllosphere bacterial and fungal microbiota in the Giant Panda National Park, China.

Analysis of microbial community composition and diversity in the rhizosphere of Salvia miltiorrhiza at different growth stages.

Salvia miltiorrhiza is a kind of medicinal plant with various pharmacological activities. Few studies on the composition and diversity of rhizosphere microbial communities at different growth stages have been conducted on Salvia miltiorrhiz; in particular, salviorrhiza grows in soil that has been continuously planted for 3 years. The purpose of this study was to understand the changes of soil physicochemical properties of Salvia miltiorrhiza at different growth stages, and to study the composition and diversity of rhizosphere microbial community at different growth stages. Illumina NovaSeq sequencing technology was used to analyze the bacterial 16S rRNA gene and the fungal ITS region in the rhizosphere soil of Salvia miltiorrhiza at different growth stages. The results showed that the dominant bacterial phyla in the Salvia miltiorrhiza rhizosphere were Proteobacteria, Bacteroidetes, Acidobacteria, Firmicutes, Actinobacteria, and Chloroflexi. The dominant fungal phyla were Ascomycota, Mortierellomycota, Basidiomycota, and Rozellomycota. During the growth of Salvia miltiorrhiza, the physical and chemical properties of soil changed. As the Salvia miltiorrhiza grew, the content of available phosphorus, available potassium, pH, nitrate nitrogen, and ammonium nitrogen significantly decreased. Ammonium nitrogen and nitrate nitrogen had a greater impact on the bacterial community structure in the rhizosphere than on the fungal community structure. The work was to reveal differences in the rhizosphere bacterial and fungal community structure during different growth stages of Salvia miltiorrhiza, further understand the changes of rhizosphere microbial ecological characteristics and soil physicochemical properties during the cultivation of Salvia miltiorrhiza.

Bacterial biogeography of the Indian Ocean.

Historically, our understanding of bacterial ecology in the Indian Ocean has been limited to regional studies that place emphasis on community structure and function within oxygen minimum zones. Thus, bacterial community dynamics across the wider Indian Ocean are largely undescribed. As part of Bio-GO-SHIP, we sequenced the 16S rRNA gene from 465 samples collected on sections I07N and I09N. We found that (i) there were 23 distinct bioregions within the Indian Ocean, (ii) the southeastern gyre had the largest gradient in bacterial alpha-diversity, (iii) the Indian Ocean surface microbiome was primarily composed of a core set of taxa, and (iv) bioregions were characterized by transitions in physical and geochemical conditions. Overall, we showed that bacterial community structure spatially delineated the surface Indian Ocean and that these microbially-defined regions were reflective of subtle ocean physical and geochemical gradients. Therefore, incorporating metrics of in-situ microbial communities into marine ecological regions traditionally defined by remote sensing will improve our ability to delineate warm, oligotrophic regions.

Strong Saharan Dust Deposition Events Alter Microbial Diversity and Composition in Sediments of High-Mountain Lakes of Sierra Nevada (Spain).

Mediterranean high-mountain lakes are being increasingly affected by strong Saharan dust deposition events. However, the ecological impacts of these severe atmospheric episodes remain largely unknown. We examined the effects of a strong Saharan dust intrusion to the Iberian Peninsula in 2022 on the physicochemical parameters and prokaryotic communities in sediments of nine high-mountain lakes of Sierra Nevada (Spain) located above 2800 m.a.s.l and in different orientations (north vs. south). A previous year (2021), with lower Saharan dust deposition with respect to 2022, was used for interannual comparisons. The strong dust deposition to the high-mountain lakes resulted in a significant increase in sediment nutrient availability which was linked to changes in the composition of prokaryotic communities. Decreases in alpha diversity and changes in beta diversity of prokaryotic communities were mainly observed in lakes located in the south compared to the north orientation likely because the former was more affected by the atmospheric dust deposition episode. Dust intrusion to the high-mountain lakes resulted in significant changes in the relative abundance of specific genera involved in important nutrient cycling processes such as phosphate solubilization, nitrogen fixation, nitrification, and denitrification. Saharan dust deposition also increased predicted microbial functionality in all lakes. Our findings show that severe atmospheric dust inputs to remote high-mountain lakes of Sierra Nevada can have significant biogeochemical and biodiversity consequences through changes in nutrient availability and prokaryotic communities in sediments of these freshwater ecosystems. This information contributes to understanding how Mediterranean high-mountain lakes of Sierra Nevada face strong intrusions of Saharan dust and their ecological consequences.