Impact of residual antibiotics on microbial decomposition of livestock manures in Eutric Regosol: Implications for sustainable nutrient recycling and soil carbon sequestration.

The land application of livestock manure has been widely acknowledged as a beneficial approach for nutrient recycling and environmental protection. However, the impact of residual antibiotics, a common contaminant of manure, on the degradation of organic compounds and nutrient release in Eutric Regosol is not well understood. Here, we studied, how oxytetracycline (OTC) and ciprofloxacin (CIP) affect the decomposition, microbial community structure, extracellular enzyme activities and nutrient release from cattle and pig manure using litterbag incubation experiments. Results showed that OTC and CIP greatly inhibited livestock manure decomposition, causing a decreased rate of carbon (28%-87%), nitrogen (15%-44%) and phosphorus (26%-43%) release. The relative abundance of gram-negative (G-) bacteria was reduced by 4.0%-13% while fungi increased by 7.0%-71% during a 28-day incubation period. Co-occurrence network analysis showed that antibiotic exposure disrupted microbial interactions, particularly among G- bacteria, G+ bacteria, and actinomycetes. These changes in microbial community structure and function resulted in decreased activity of urease, ß-1,4-N-acetyl-glucosaminidase, alkaline protease, chitinase, and catalase, causing reduced decomposition and nutrient release in cattle and pig manures. These findings advance our understanding of decomposition and nutrient recycling from manure-contaminated antibiotics, which will help facilitate sustainable agricultural production and soil carbon sequestration.

Exploring the distribution and co-occurrence of rpf-like genes and nitrogen-cycling genes in water reservoir sediments.

Water reservoir sediments represent a distinct habitat that harbors diverse microbial resources crucial for nitrogen cycling processes. The discovery of resuscitation promoting factor (Rpf) has been recognized as a crucial development in understanding the potential of microbial populations. However, our understanding of the relationship between microorganisms containing rpf-like genes and nitrogen-cycling functional populations remains limited. The present study explored the distribution patterns of rpf-like genes and nitrogen-cycling genes in various water reservoir sediments, along with their correlation with environmental factors. Additionally, the co-occurrence of rpf-like genes with genes associated with the nitrogen cycle and viable but non-culturable (VBNC) formation was investigated. The findings indicated the ubiquitous occurrence of Rpf-like domains and their related genes in the examined reservoir sediments. Notably, rpf-like genes were predominantly associated with Bradyrhizobium, Nitrospira, and Anaeromyxobacter, with pH emerging as the primary influencing factor for their distribution. Genera such as Nitrospira, Bradyrhizobium, Anaeromyxobacter, and Dechloromonas harbor the majority of nitrogen-cycling functional genes, particularly denitrification genes. The distribution of nitrogen-cycling microbial communities in the reservoir sediments was mainly influenced by pH and NH4 +. Notably, correlation network analysis revealed close connections between microorganisms containing rpf-like genes and nitrogen-cycling functional populations, as well as VBNC bacteria. These findings offer new insights into the prevalence of rpf-like genes in the water reservoir sediments and their correlation with nitrogen-cycling microbial communities, enhancing our understanding of the significant potential of microbial nitrogen cycling.

Host specialization and spatial divergence of bacteria associated with Peltigera lichens promote landscape gamma diversity.

BACKGROUND: Lichens are micro-ecosystems relying on diverse microorganisms for nutrient cycling, environmental adaptation, and structural support. We investigated the spatial-scale dependency of factors shaping the ecological processes that govern lichen-associated bacteria. We hypothesize that lichens function as island-like habitats hosting divergent microbiomes and promoting landscape gamma-diversity. Three microenvironments -thalli, substrates, and neighboring soils- were sampled from four geographically overlapping species of Peltigera cyanolichens, spanning three bioclimatic zones in the Chilean Patagonia, to determine how bacterial diversity, assembly processes, ecological drivers, interaction patterns, and niche breadth vary among Peltigera microenvironments on a broad geographical scale. RESULTS: The hosts' phylogeny, especially that of the cyanobiont, alongside climate as a secondary factor, impose a strong ecological filtering of bacterial communities within Peltigera thalli. This results in deterministically assembled, low diverse, and phylogenetically convergent yet structurally divergent bacterial communities. Host evolutionary and geographic distances accentuate the divergence in bacterial community composition of Peltigera thalli. Compared to soil and substrate, Peltigera thalli harbor specialized and locally adapted bacterial taxa, conforming sparse and weak ecological networks. CONCLUSIONS: The findings suggest that Petigera thalli create fragmented habitats that foster landscape bacterial gamma-diversity. This underscores the importance of preserving lichens for maintaining a potential reservoir of specialized bacteria.

Seasonal dynamics of free-living (FL) and particle-attached (PA) bacterial communities in a plateau reservoir.

In terms of lifestyle, bacterioplankton can be classified as free-living (FL) and particle-attached (PA) forms, and both play essential roles in biogeochemical cycling in aquatic ecosystems. Structure, distribution, and community assembly of FL and PA bacteria in plateau riverine waterbodies are largely unknown. Therefore, we explored the seasonal dynamics of FLand PA bacterial communities in the Wujiangdu reservoir, Yungui Plateau using 16S rRNA gene high-throughput sequencing. Results revealed there was a significant environmental heterogeneity in Wujiangdu reservoir seasonally. The dominant phylum was Actinomycetota for FL and Pseudomonadota for PA bacteria. Species richness and diversity was higher in autumn and winter compared to spring and summer. In general, PA diversity was greater than FL, but with some temporal variations. Species turnover was the major contributor to ß-diversity of both FL and PA lifestyles, and significant differences were noticed between FL and PA bacterial community composition. Distinct co-occurrence network patterns implied that more connections exist between FL bacteria, while more complex PA networks were in parallel to their greater diversity and stronger interactions in biofilms on particles. Dispersal limitation was the major driving force for both FL and PA bacterial community assembly. Deterministic processes were of relatively low importance, with homogeneous selection for FL and heterogeneous selection for PA bacteria. Temperature was the most important environmental driver of seasonal bacterial dynamics, followed by nitrate for FL and Secchi depth for PA bacteria. This study allows for a better understanding of the temporal variability of different bacteria lifestyles in reservoirs in the vulnerable and rapidly changing plateau environment, facilitating further microbial research related to global warming and eutrophication.

Non-invasive ventilation restores the gut microbiota in rats with acute heart failure.

Heart failure (HF) is an increasingly prevalent disease in humans; it induces multiple symptoms and damages health. The animal gut microbiota has critical roles in host health, which might be related to HF symptoms. Currently, several options are used to treat HF, including non-invasive ventilation (NIV). However, studies on gut microbiota responses to acute HF and associated treatments effects on gut communities in patients are scarce. Here, short-term (1 week after treatments) and long-term (3 months after treatment) variations in gut microbiota variations in rats with acute HF treated were examined NIV through high-throughput sequencing of the bacterial 16S rRNA gene. Through comparison of gut microbiota alpha diversity, it was observed lower gut microbiota richness and diversity in animals with acute HF than in normal animals. Additionally, beta-diversity analysis revealed significant alterations in the gut microbiota composition induced by acute HF, as reflected by increased Firmicutes/Bacteroidetes (F/B) ratios and Proteobacteria enrichment. When network analysis results were combined with the null model, decreased stability and elevated deterministic gut microbiota assemblies were observed in animals with acute HF. Importantly, in both short- and long-term periods, NIV was found to restore gut microbiota dysbiosis to normal states in acute HF rats. Finally, it was shown that considerable gut microbiota variations existed in rats with acute HF, that underlying microbiota mechanisms regulated these changes, and confirmed that NIV is suitable for HF treatment. In future studies, these findings should be validated with different model systems or clinical samples.

Spartina alterniflora invasion reduces soil microbial diversity and weakens soil microbial inter-species relationships in coastal wetlands.

Soil microorganisms play a crucial role in the plant invasion process, acting as both drivers of and responders to plant invasion. However, the effects of plant invasion on the complexity and stability of co-occurrence networks of soil microbial communities remain unclear. Here, we investigated how the invasion of Spartina alterniflora affected the diversity, composition, and co-occurrence networks of soil bacterial and fungal communities in the Yellow River Delta, China. Compared to the native plant (Suaeda salsa), S. alterniflora invasion decreased the α-diversity of soil bacterial communities but did not affect that of fungal communities. The ß-diversity of soil bacterial and fungal communities under S. salsa and S. alterniflora habitats also differed dramatically. S. alterniflora invasion increased the relative abundance of the copiotrophic phylum Bacteroidota, whereas decreased the relative abundances of the oligotrophic phyla Acidobacteriota and Gemmatimonadota. Additionally, the relative abundance of Chytridiomycota, known for its role in degrading recalcitrant organic matter, increased substantially within the soil fungal community. Functional predictions revealed that S. alterniflora invasion increased the relative abundance of certain soil bacteria involved in carbon and nitrogen cycling, including aerobic chemoheterotrophy, nitrate reduction, and nitrate respiration. More importantly, S. alterniflora invasion reduced the complexity and stability of both soil bacterial and fungal community networks. The shifts in soil microbial community structure and diversity were mainly induced by soil available nutrients and soil salinity. Overall, our study highlights the profound impacts of S. alterniflora invasion on soil microbial communities, which could further indicate the modification of ecosystem functioning by invasive species.

Heterogenetic mechanism in multidimensional pit mud with different fermentation years: From microbial structure dynamic succession to metabolism phenotypes.

Pit mud (PM) is fermenting agents in the strong-flavor baijiu (SFB) production. In this paper, the discrepancies in fermentation parameters, microbial community succession patterns and metabolic phenotypes were compared in multidimensional PMs. The results showed that pyruvic acid, succinic acid, S-Acetyldihydrolipoamide-E, glycerol and glyceric acid were the key metabolites responsible for the metabolic differences between the 2-, 30-,100- and 300-year multidimensional PMs, while the butanoic acid, heptyl, heptanoic acid, heptanoic acid ethyl ester, hexanoic acid and octanoic acid were the key differential flavor compounds in the 2-, 30-,100- and 300-year multidimensional PMs. Concurrently, the diversity and abundance of microbial community also exhibited significant differences between the new and old multidimensional PMs, the assembly pattern of bacterial communities changed from deterministic to stochasticity from lower (bottom of the pit and under the huangshui fluid) to upper PM (up the huangshui fluid and top of the pit). Key microorganisms related to the succession process of the lower PM were Clostridium, Methanobacterium, Petrimonas, Lactobacillus, Methanobrevibacter, Bellilinea, Longilinea, Bacillus. In contrast, the upper PM were Caproicibacter, Longilinea, Lactobacillus, Proteinphilum, Methanobrevibacter, Methanobacterium, Methanobacteriaceae, Petrimonas, Bellilinea and Atopobium. Redundancy analysis (RDA) indicated that the key environmental factors regulating the succession of microbial in upper PM were lactic acid, moisture, pH and available phosphorus. In contrast, the lower was lactic acid, acetic acid and ammonia N. Based on these results, heterogeneous mechanisms between new and old multidimensional PMs were explored, providing a theoretical support for improving the quality of new PM.

Metabarcoding and co-occurrence network reveal significant effects of mariculture on benthic eukaryotic microalgal community: A case study in Daya Bay of the South China Sea.

Benthic eukaryotic microalgae were analyzed by metabarcoding the partial 18S rRNA gene in Daya Bay bi-monthly in 2021. Altogether 941 eukaryotic microalgal OTUs were detected, belonging to 27 classes of 8 phyla. Dinophyta and Chlorophyta were the dominant phyla. Microalgal community in the mariculture zone differed significantly from those in non-mariculture zone, reflected by low alpha diversity indexes and increasing abundance and richness of chlorophytes and correspondingly decreasing of dinoflagellates. The abundant occurrences of the pico- and nano-sized taxa such as the chlorophyte Picochlorum in the mariculture zone suggested that nutrient enrichment might result in the miniaturization of the benthic eukaryotic microalgae. The co-occurrence network suggested more negative interactions between taxa in the mariculture zone. A total of 41 algal bloom and/or harmful algal bloom (HAB) species were detected in this study, suggesting a high potential risk of HABs in Daya Bay, especially for the recurrent bloom species Scrippsiella acuminata.

Host-associated helminth diversity and microbiome composition contribute to anti-pathogen defences in tropical frogs impacted by forest fragmentation.

Habitat fragmentation can negatively impact wildlife populations by simplification of ecological interactions, but little is known about how these impacts extend to host-associated symbiotic communities. The symbiotic communities of amphibians play important roles in anti-pathogen defences, particularly against the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd). In this study, we analyse the role of macroparasitic helminth communities in concert with microbial communities in defending the host against Bd infection within the context of forest fragmentation. We found that skin microbial and helminth communities are disrupted at fragmented habitats, while gut microbiomes appear more resilient to environmental change. We also detected potential protective roles of helminth diversity and anti-pathogen microbial function in limiting Bd infection. Microbial network analysis revealed strong patterns of structure in both skin and gut communities, with helminths playing central roles in these networks. We reveal consistent roles of microbial and helminth diversity in driving host-pathogen interactions and the potential implications of fragmentation on host fitness.

How the root bacterial community of Ficus tikoua responds to nematode infection: enrichments of nitrogen-fixing and nematode-antagonistic bacteria in the parasitized organs.

Plant-parasitic nematodes (PPNs) are among the most damaging pathogens to host plants. Plants can modulate their associated bacteria to cope with nematode infections. The tritrophic plant-nematode-microbe interactions are highly taxa-dependent, resulting in the effectiveness of nematode agents being variable among different host plants. Ficus tikoua is a versatile plant with high application potential for fruits or medicines. In recent years, a few farmers have attempted to cultivate this species in Sichuan, China, where parasitic nematodes are present. We used 16S rRNA genes to explore the effects of nematode parasitism on root-associated bacteria in this species. Our results revealed that nematode infection had effects on both endophytic bacterial communities and rhizosphere communities in F. tikoua roots, but on different levels. The species richness increased in the rhizosphere bacterial communities of infected individuals, but the community composition remained similar as compared with that of healthy individuals. Nematode infection induces a deterministic assembly process in the endophytic bacterial communities of parasitized organs. Significant taxonomic and functional changes were observed in the endophytic communities of root knots. These changes were characterized by the enrichment of nitrogen-fixing bacteria, including Bradyrhizobium, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, and nematode-antagonistic bacteria, such as Pseudonocardia, Pseudomonas, Steroidobacter, Rhizobacter, and Ferrovibrio. Our results would help the understanding of the tritrophic plant-nematode-bacterium interactions in host plants other than dominant crops and vegetables and would provide essential information for successful nematode management when F. tikoua were cultivated on large scales.

[Interaction Effects of Vegetation and Soil Factors on Microbial Communities in Alpine Steppe Under Degradation].

To clarify the regulating effect of vegetation and soil factors on microbial communities in the alpine steppe under degradation on the Qinghai-Xizang Plateau, the alpine steppe in the Sanjiangyuan area of the Qinghai-Tibet Plateau was chosen. We analyzed the differences in vegetation and soil factors in different stages of degradation （non-degradation, moderate degradation, and severe degradation） and detected the variations in microbial community characteristics in the alpine steppe under different degradation stages using high-throughput sequencing technology. Eventually, redundancy analysis （RDA） and multiple regression matrixes （MRM） based on the similarity or dissimilarity matrix were used to identify key environmental factors regulating microbial （bacterial and fungal） community changes under degradation. The results showed that the degradation of the alpine steppe significantly changed the community coverage, height, biomass, and important value of graminae； significantly reduced the contents of soil organic matter, total nitrogen, total phosphorus, and silt； and increased the soil bulk density and sand content. Degradation did not change the composition of bacteria and fungi, but their composition proportions changed and also resulted in the loss of microbial richness （Chao1 index and Richness index） but did not significantly change the microbial diversity （Shannon index）. With the occurrence of degradation, the vegetation characteristics, soil physicochemical properties, and microbial diversity showed a consistent change trend. Combined with the characteristics of the network topology changes （the number of nodes and clustering coefficient significantly decreased）, it was found that degradation of the alpine steppe led to the decline of interspecies interactions, decentralization of network, and homogenization of microorganisms, but the cooperation relations among the species were maintained （positive correlation connections accounted for more than 90% in all degradation stages）. Under the alpine steppe degradation, the vegetation-soil interaction had the greatest effect on soil bacterial community, whereas soil physicochemical properties had the greatest influence on soil fungal community. Specifically, vegetation community height, biomass, and soil bulk density were the mutual factors regulating soil microorganisms, whereas the vegetation Simpson index, important value of graminae, soil total phosphorus, total potassium, and silt content were the unique factors affecting the soil bacterial community, and soil pH and total nitrogen content were the particular factors affecting the soil fungal community.

Leaf Health Status Regulates Endophytic Microbial Community Structure, Network Complexity, and Assembly Processes in the Leaves of the Rare and Endangered Plant Species Abies fanjingshanensis.

The rare and endangered plant species Abies fanjingshanensis, which has a limited habitat, a limited distribution area, and a small population, is under severe threat, particularly due to poor leaf health. The plant endophytic microbiome is an integral part of the host, and increasing evidence indicates that the interplay between plants and endophytic microbes is a key determinant for sustaining plant fitness. However, little attention has been given to the differences in the endophytic microbial community structure, network complexity, and assembly processes in leaves with different leaf health statuses. Here, we investigated the endophytic bacterial and fungal communities in healthy leaves (HLs) and non-healthy leaves (NLs) of A. fanjingshanensis using 16S rRNA gene and internal transcribed spacer sequencing and evaluated how leaf health status affects the co-occurrence patterns and assembly processes of leaf endophytic microbial communities based on the co-occurrence networks, the niche breadth index, a neutral community model, and C-score metrics. HLs had significantly greater endophytic bacterial and fungal abundance and diversity than NLs, and there were significant differences in the endophytic microbial communities between HLs and NLs. Leaf-health-sensitive endophytic microbes were taxonomically diverse and were mainly grouped into four ecological clusters according to leaf health status. Poor leaf health reduced the complexity of the endophytic bacterial and fungal community networks, as reflected by a decrease in network nodes and edges and an increase in degrees of betweenness and assortativity. The stochastic processes of endophytic bacterial and fungal community assembly were weakened, and the deterministic processes became more important with declining leaf health. These results have important implications for understanding the ecological patterns and interactions of endophytic microbial communities in response to changing leaf health status and provide opportunities for further studies on exploiting plant endophytic microbes to conserve this endangered Abies species.

Soil Fungal Community Differences in Manual Plantation Larch Forest and Natural Larch Forest in Northeast China.

Soil fungal communities are pivotal components in ecosystems and play an essential role in global biogeochemical cycles. In this study, we determined the fungal communities of a natural larch forest and a manual plantation larch forest in Heilongjiang Zhongyangzhan Black-billed Capercaillie Nature Reserve and Gala Mountain Forest using high-throughput sequencing. The interactions between soil fungal communities were analysed utilising a co-occurrence network. The relationship between soil nutrients and soil fungal communities was determined with the help of Mantel analysis and a correlation heatmap. The Kruskal-Wallis test indicated that different genera of fungi differed in the two forest types. The results show that there was a significant change in the alpha diversity of soil fungal communities in both forests. In contrast, nonmetric multidimensional scaling (NMDS) analysis showed significant differences in the soil fungal community structures between the manual plantation larch forest and the natural larch forest. The soil fungal co-occurrence network showed that the complexity of the soil fungal communities in the manual plantation larch forest decreased significantly compared to those in the natural larch forest. A Mantel analysis revealed a correlation between the soil fungal co-occurrence network, the composition of soil fungi, and soil nutrients. The RDA analysis also showed that AN, TK, and pH mainly influenced the soil fungal community. The null model test results showed the importance of stochastic processes in soil fungal community assembly in manual plantation larch forests. Overall, this study enhances our understanding of the differences in soil fungal communities in manual plantation larch forests and natural larch forests, providing insights into their sustainable management. It also serves as a reminder that the ecological balance of natural ecosystems is difficult to restore through human intervention, so we need to protect natural ecosystems.

Structure and Diversity of Endophytic Bacteria in Maize Seeds and Germinating Roots.

Seed endophytes in maize, which facilitate the transmission of microorganisms from one plant generation to the next, may play a crucial role in plant protection and growth promotion. This study aimed to investigate the effects of various maize varieties on the communities of endophytic bacteria in seeds and germinating roots. This study utilized Illumina high-throughput sequencing technology to examine the structural and diversity differences of endophytic bacterial communities within seed maize (BY1507), silage maize (QQ446), and wild maize (Teosinte) in both seeds and germinating roots. The results showed that 416 bacterial genera were detected, with Pantoea, Lachnospiraceae, Pararhizobium, Enterobacteriaceae, Stenotrophomonas, and Pseudonocardia being the most prevalent (relative abundance > 10%) at the genus level. No significant difference was observed in diversity indices (Chao1, ACE, Shannon, and Simpson) of seed endophytes among BY1507, QQ446, and Teosinte. The Shannon and Simpson indices for the germinating root endophyte from the wild variety (Teosinte) were significantly higher than the domesticated varieties (BY1507 and QQ446). PCoA revealed a notable overlap in the endophytic bacterial communities from the seeds of BY1507, QQ446, and Teosinte. Yet, clustering patterns were found. Co-occurrence network analysis showed that BY1507, QQ446, and Teosinte share a notable proportion of shared endophytic bacteria (>30%) between the seeds and germinating roots. This investigation elucidates the characteristics of endophytic microbial communities of seeds and germinating roots with seed maize, silage maize, and wild maize, offering data for future research on the physiological ecological adaptation of these endophytic microbial communities.

Stable microbial community diversity across large-scale Antarctic water masses.

The distinctive environmental attributes of the Southern Ocean underscore the indispensability of microorganisms in this region. We analyzed 208 samples obtained from four separate layers (Surface, Deep Chlorophyll Maximum, Middle, and Bottom) in the neighboring seas of the Antarctic Peninsula and the Cosmonaut Sea to explore variations in microbial composition, interactions and community assembly processes. The results demonstrated noteworthy distinctions in alpha and beta diversity across diverse communities, with the increase in water depth, a gradual rise in community diversity was observed. In particular, the co-occurrence network analysis exposed pronounced microbial interactions within the same water mass, which are notably stronger than those observed between different water masses. Co-occurrence network complexity was higher in the surface water mass than in the bottom water mass. Yet, the surface water mass exhibited greater network stability. Moreover, in the phylogenetic-based ß-nearest taxon distance analyses, deterministic processes were identified as the primary factors influencing community assembly in Antarctic microorganisms. This study contributes to exploring diversity and assembly processes under the complex hydrological conditions of Antarctica.

Linking active rectal mucosa-attached microbiota to host immunity reveals its role in host-pathogenic STEC O157 interactions.

The rectal-anal junction (RAJ) is the major colonization site of Shiga toxin-producing Escherichia coli (STEC) O157 in beef cattle, leading to transmission of this foodborne pathogen from farms to food chains. To date, there is limited understanding regarding whether the mucosa-attached microbiome has a profound impact on host-STEC interactions. In this study, the active RAJ mucosa-attached microbiota and its potential role in host immunity-STEC commensal interactions were investigated using RAJ mucosal biopsies collected from calves orally challenged with two STEC O157 strains with or without functional stx2a (stx2a+ or stx2a-). The results revealed that shifts of microbial diversity, topology, and assembly patterns were subjected to stx2a production post-challenge and Paeniclostridium and Gallibacterium were the keystone taxa for both microbial interactions and assembly. Additional mucosal transcriptome profiling showed stx2a-dependent host immune responses (i.e. B- and T-cell signaling and antigen processing and presentation) post-challenge. Further integrated analysis revealed that mucosa-attached beneficial microbes (i.e. Provotella, Faecalibacterium, and Dorea) interacted with host immune genes pre-challenge to maintain host homeostasis; however, opportunistic pathogenic microbes (i.e. Paeniclostridium) could interact with host immune genes after the STEC O157 colonization and interactions were stx2a-dependent. Furthermore, predicted bacterial functions involved in pathogen (O157 and Paeniclostridium) colonization and metabolism were related to host immunity. These findings suggest that during pathogen colonization, host-microbe interactions could shift from beneficial to opportunistic pathogenic bacteria driven and be dependent on the production of particular virulence factors, highlighting the potential regulatory role of mucosa-attached microbiota in affecting pathogen-commensal host interactions in calves with STEC O157 infection.

Exploring seasonal variations, assembly dynamics, and relationships of bacterial communities in different habitats of marine ranching.

Offshore coastal marine ranching ecosystems provide habitat for diverse and active bacterial communities. In this study, 16S rRNA gene sequencing and multiple bioinformatics methods were applied to investigate assembly dynamics and relationships in different habitats. The higher number of edges in the water network, more balanced ratio of positive and negative links, and more keystone species included in the co-occurrence network of water. Stochastic processes dominated in shaping gut and sediment community assembly (R2 < 0.5), while water bacterial community assembly were dominated by deterministic processes (R2 > 0.5). Dissimilarity-overlap curve model indicated that the communities in different habitats have general dynamics and interspecific interaction (P < 0.001). Bacterial source-tracking analysis revealed that the gut was more similar to the sediment than the water bacterial communities. In summary, this study provides basic data for the ecological study of marine ranching through the study of bacterial community dynamics.

Tobacco crop rotation enhances the stability and complexity of microbial networks.

Introduction: The effects of continuous cropping and rotation cropping, two important tobacco cultivation practices, on soil microbial communities at different stages remain unclear. Different planting patterns have been shown to influence soil physical and chemical properties, which in turn can affect the composition and diversity of soil microbial communities. Methods: In order to investigate the impact of different planting methods on soil microbial community structure, we selected two representative planting methods: continuous cropping (tobacco) and rotational cropping (tobacco-maize). These methods were chosen as the focal points of our research to explore the potential effects on soil microbial communities. High-throughput sequencing technology was employed to investigate the structure of soil microbial communities, as well as their relationships with soil environmental factors, by utilizing the 16S rRNA, ITS, and 18S genes. Furthermore, the interaction among microorganisms was explored through the application of the Random Matrix Theory (RMT) molecular ecological network approach. Results: There was no significant difference in α diversity, but significant difference in ß diversity based on Jaccard distance test. Compared to continuous cropping, crop rotation significantly increased the abundance of beneficial prokaryotes Verrucomicrobia and Rhodanobacter. These findings indicate that crop rotation promotes the enrichment of Verrucomicrobia and Rhodanobacter in the soil microbial community. AP and NH4-N had a greater effect on the community structure of prokaryotes and fungi in tobacco soil, while only AP had a greater effect on the community structure of protist. Molecular ecological network analysis showed that the network robustness and Cohesion of rotation were significantly higher than that of continuous cropping, indicating that the complexity and stability of molecular ecological networks were higher in the rotational, and the microbial communities cooperated more effectively, and the community structure was more stable. Discussion: From this point of view, rotational cropping is more conducive to changing the composition of soil microbial community, enhancing the stability of microbial network structure, and enhancing the potential ecological functions in soil.

The Potential of Co-Fermentation of Whole-Plant Cassava with Piper sarmentosum: A Comprehensive Study of Fermentation Quality, Antioxidant Activity, Bacterial Community Structure, and Microbial Ecological Networks in Novel Foods.

The objective of this study was to explore the preservation of food products through the co-fermentation of whole-plant cassava and Piper sarmentosum (PS) without additives. We assessed fermentation quality, antioxidant activity, bacterial community structure, function profile, and microbial ecological network features. Our results demonstrate that co-fermentation of whole-plant cassava with 10% PS significantly improves food quality. The co-fermented samples exhibited enhanced lactic acid concentrations and increased antioxidant activity, with reduced pH values and concentrations of acetic acid, butyric acid, and ammonia-N(NH3-N) compared to whole-plant cassava fermented alone. In addition, PS addition also optimized microbial community structure by elevating the total abundance of lactic acid bacteria and influenced bacterial predicted functions. Furthermore, our analysis of co-occurrence networks reveals that co-fermentation impacts microbial network features, including module numbers and bacterial relative abundances, leading to altered complexity and stability of the networks. Moreover, out study also highlights the impact of ferment undesirable bacteria like Pseudomonas aeruginosa and unclassified_Muribaculaceae playing crucial roles in microbial network complexity and stability. These findings provide valuable insights into the anaerobic fermentation process and offers strategies for regulating food fermentation quality.

Fertilization regime changes rhizosphere microbial community assembly and interaction in Phoebe bournei plantations.

Fertilizer input is one of the effective forest management practices, which improves soil nutrients and microbial community compositions and promotes forest productivity. However, few studies have explored the response of rhizosphere soil microbial communities to various fertilization regimes across seasonal dynamics. Here, we collected the rhizosphere soil samples from Phoebe bournei plantations to investigate the response of community assemblages and microbial interactions of the soil microbiome to the short-term application of four typical fertilizer practices (including chemical fertilizer (CF), organic fertilizer (OF), compound microbial fertilizer (CMF), and no fertilizer control (CK)). The amendments of organic fertilizer and compound microbial fertilizer altered the composition of rhizosphere soil bacterial and fungal communities, respectively. The fertilization regime significantly affected bacterial diversity rather than fungal diversity, and rhizosphere fungi responded more sensitively than bacteria to season. Fertilization-induced fungal networks were more complex than bacterial networks. Stochastic processes governed both rhizosphere soil bacterial and fungal communities, and drift and dispersal limitation dominated soil fungal and bacterial communities, respectively. Collectively, these findings demonstrate contrasting responses to community assemblages and interactions of rhizosphere bacteria and fungi to fertilizer practices. The application of organic fertilization strengthens microbial interactions and changes the succession of key taxa in the rhizosphere habitat. KEY POINTS: • Fertilization altered the key taxa and microbial interaction • Organic fertilizer facilitated the turnover of rhizosphere microbial communities • Stochasticity governed soil fungal and bacterial community assembly.