Understanding host-microbial interactions in rumen：searching the best opportunity for microbiota manipulation

Ruminants utilize a wide variety of dietary substrates that are not digestible by the mammals, through microbial fermentation taking place in the rumen. Recent advanced molecular based approaches have allowed the characterization of rumen microbiota and its compositional changes under various treatment conditions.However, the knowledge is still limited on the impacts of variations in the rumen microbiota on host biology and function. This review summarizes the information to date on host-microbial interactions in the rumen and how we can apply such information to seek the opportunities to enhance the animal performance through manipulating the rumen function.

Gut microbial interactions based on network construction and bacterial pairwise cultivation

Association networks are widely applied for the prediction of bacterial interactions in studies of human gut microbiomes.However,the experimental validation of the predicted interactions is challenging due to the complexity of gut microbiomes and the limited number of cultivated bacteria.In this study,we addressed this challenge by integrating in vitro time series network(TSN)associations and cocultivation of TSN taxon pairs.Fecal samples were collected and used for cultivation and enrichment of gut microbiome on YCFA agar plates for 13 days.Enriched cells were harvested for DNA extraction and metagenomic sequencing.A total of 198 metagenome-assembled genomes(MAGs)were recovered.Temporal dynamics of bacteria growing on the YCFA agar were used to infer microbial association networks.To experimentally validate the interactions of taxon pairs in networks,we selected 24 and 19 bacterial strains from this study and from the previously established human gut microbial biobank,respectively,for pairwise co-cultures.The co-culture experiments revealed that most of the interactions between taxa in networks were identified as neutralism(51.67%),followed by commensalism(21.67%),amensalism(18.33%),competition(5%)and exploitation(3.33%).Genome-centric analysis further revealed that the commensal gut bacteria(helpers and beneficiaries)might interact with each other via the exchanges of amino acids with high biosynthetic costs,short-chain fatty acids,and/or vitamins.We also validated 12 beneficiaries by adding 16 additives into the basic YCFA medium and found that the growth of 66.7%of these strains was significantly promoted.This approach provides new insights into the gut microbiome complexity and microbial interactions in association networks.Our work highlights that the positive relationships in gut microbial communities tend to be overestimated,and that amino acids,short-chain fatty acids,and vitamins are contributed to the positive relationships.

Responses of microbial interactions to elevated salinity in activated sludge microbial community

Biological treatment processes are critical for sewage purification,wherein microbial interactions are tightly associated with treatment performance.Previous studies have focused on assessing how environmental factors(such as salinity)affect the diversity and composition of the microbial community but ignore the connections among microorganisms.Here,we described the microbial interactions in response to elevated salinity in an activated sludge system by performing an association network analysis.It was found that higher salinity resulted in low microbial diversity,and small,complex,more competitive overall networks,leading to poor performance of the treatment process.Subnetworks of major phyla(Proteobacteria,Bacteroidetes,and Chloroflexi)and functional bacteria(such as AOB,NOB and denitrifiers)differed substantially under elevated salinity process.Compared with subnetworks of Nitrosomonadaceae,Nitrosomonas(AOB)made a greater contribution to nitrification under higher salinity(especially 3%)in the activated sludge system.Denitrifiers established more proportion of cooperative relationships with other bacteria to resist 3%salinity stress.Furthermore,identified keystone species playing crucial roles in maintaining process stability were dynamics and less abundant under salinity disturbance.Knowledge gleaned from this study deepened our understanding of microbial interaction in response to elevated salinity in activated sludge systems.

Soil biofilms:microbial interactions,challenges,and advanced techniques for ex-situ characterization

Soil is inhabited by a myriad of microorganisms,many of which can form supracellular structures,called biofilms,comprised of surface-associated microbial cells embedded in hydrated extracellular polymeric substance that facilitates adhesion and survival.Biofilms enable intensive inter-and intra-species interactions that can increase the degradation efficiency of soil organic matter and materials commonly regarded as toxins.Here,we first discuss organization,dynamics and properties of soil biofilms in the context of traditional approaches to probe the soil microbiome.Social interactions among bacteria,such as cooperation and competition,are discussed.We also summarize different biofilm cultivation devices in combination with optics and fluorescence microscopes as well as sequencing techniques for the study of soil biofilms.Microfluidic platforms,which can be applied to mimic the complex soil environment and study microbial behaviors at the microscale with highthroughput screening and novel measurements,are also highlighted.This review aims to highlight soil biofilm research in order to expand the current limited knowledge about soil microbiomes which until now has mostly ignored biofilms as a dominant growth form.

Chrysanthemum Growth Gains from Beneficial Microbial Interactions and Fertility Improvements in Soil Under Protected Cultivation

An investigation was undertaken to analyse the influence of microbial inoculants on growth and enzyme activities elicited, and soil microbiome of two varieties of Chrysanthemum morifolium Ramat, which were grown under protected mode of cultivation. Rhizosphere soil sampling at 45 and 90 DAT(days after transplanting of cuttings) revealed up to four- to five-fold enhancement in the activity of defence-, and pathogenesisrelated, and antioxidant enzymes, relative to the uninoculated control. Plant growth and soil microbial parameters, especially soil microbial biomass carbon and potential nitrification exhibited significant increases over control. Available soil nitrogen concentrations showed 40%–44% increment in inoculated treatments. Scanning electron microscopy of the root tissues revealed biofilm-like aggregates and individual short bits of cyanobacterial filaments. Analyses of DGGE profiles of archaeal and bacterial communities did not show temporal variations(between 45 and 90 DAT). However,distinct influences on the number and abundance of phylotypes due to microbial inoculants were recorded. The inoculants — Cyanobacterial consortium(BF1- 4) and Anabaena sp.–Trichoderma sp. biofilm(An-Tr) were particularly promising in terms of the plant and soil related parameters,and remained distinct in the DGGE profiles generated. The effect of Trichoderma viride–Azotobacter biofilm on soil bacterial and archaeal communities was unique and distinct as a separate cluster. This study highlights that microbial inoculants exert positive effects, which are specific even to the rhizosphere soil microbiome of chrysanthemum varieties tested. Such inoculants can serve as soil fertility enhancing options in protected floriculture.

Anaerobic ammonia oxidizing bacteria： ecological distribution, metabolism, and microbial interactions

Anammox （ANaerobic AMMonia OXidation） is a newly discovered pathway in the nitrogen cycle. This discovery has increased our knowledge of the global nitrogen cycle and triggered intense interest for anammox-based applications. Anammox bacteria are almost ubiquitous in the suboxic zones of almost all types of natural ecosystems and contribute significant to the global total nitrogen loss. In this paper, their ecological distributions and contributions to the nitrogen loss in marine, wetland, terrestrial ecosystems, and even extreme environments were reviewed. The unique metabolic mechanism of anammox bacteria was well described, including the particular cellular structures and genome compositions, which indicate the special evolutionary status of anammox bacteria. Finally, the ecological interactions among anammox bacteria and other organisms were discussed based on substrate availability and spatial organizations. This review attempts to summarize the fundamental understanding of anammox, provide an up-to-date summary of the knowledge of the overall anammox status, and propose future prospects for anammox. Based on novel findings, the metagenome has become a powerful tool for the genomic analysis of communities containing anammox bacteria; the metabolic diversity and biogeochemistry in the global nitrogen budget require more comprehensive studies.

Mixing regime shapes the community assembly process,microbial interaction and proliferation of cyanobacterial species Planktothrix in a stratified lake

Lake mixing influences aquatic chemical properties and microbial community composition,and thus,we hypothesized that it would alter microbial community assembly and interac-tion.To clarify this issue,we explored the community assembly processes and cooccurrence networks in four seasons at two depths(epilimnion and hypolimnion)in a mesotrophic and stratified lake(Chenghai Lake),which formed stratification in the summer and turnover in the winter.During the stratification period,the epilimnion and hypolimnion went through contrary assembly processes but converged to similar assembly patterns in the mixing pe-riod.In a highly homogeneous selection environment,species with low niche breadth were filtered,resulting in decreased species richness.Water mixing in the winter homogenized the environment,resulting in a simpler microbial cooccurrence network.Interestingly,we observed a high abundance of the cyanobacterial genus Planktothrix in the winter,proba-bly due to nutrient redistribution and Planktothrix adaptivity to the winter environment in which mixing played important roles.Our study provides deeper fundamental insights into how environmental factors influence microbial community structure through community assembly processes.

Enhanced organic degradation and microbial community cooperation by inoculating Bacillus licheniformis in low temperature composting

Microbial activity and interaction are the important driving factors in the start-up phase of food waste composting at low temperature.The aim of this study was to explore the effect of inoculating Bacillus licheniformis on the degradation of organic components and the potential microbe-driven mechanism from the aspects of organic matter degradation,enzyme activity,microbial community interaction,and microbial metabolic function.The results showed that after inoculating B.licheniformis,temperature increased to 47.8℃ on day2,and the degradation of readily degraded carbohydrates(RDC)increased by 31.2%,and the bioheat production increased by 16.5%.There was an obvious enhancement of extracellular enzymes activities after inoculation,especially amylase activity,which increased by 7.68 times on day 4.The inoculated B.licheniformis colonized in composting as key genus in the start-up phase.Modular network analysis and Mantel test indicated that inoculation drove the cooperation between microbial network modules who were responsible for various organic components(RDC,lipid,protein,and lignocellulose)degradation in the start-up phase.Metabolic function prediction suggested that carbohydrate metabolisms including starch and sucrose metabolism,glycolysis/gluconeogenesis,pyruvate metabolism,etc.,were improved by increasing the abundance of related functional genes after inoculation.In conclusion,inoculating B.licheniformis accelerated organic degradation by driving the cooperation between microbial network modules and enhancing microbial metabolism in the start-up phase of composting.

High nitrogen fertilizer input enhanced the microbial network complexity in the paddy soil

N fertilizer altered bacterial community compositions by changing soil nutrients.•Bacterial ammonia oxidation became predominated with the increasing N rate.•Excessive N input caused the information of a more complex microbial network.•Intensified microbial competition by excessive N was due to negative link increase.Nitrogen(N)fertilization drives the structure and function of soil microbial communities,which are crucial for regulating soil biogeochemical cycling and maintaining ecosystem stability.Despite the N fertilizer effects on soil microbial composition and diversity have been widely investigated,it is generally overlooked that ecosystem processes are carried out via complex associations among microbiome members.Here,we examined the effects of five N fertilization levels(0,135,180,225,and 360 kg N ha−1)on microbial co-occurrence networks and key functional taxa such as ammonia-oxidizers in paddy soils.The results showed that N addition altered microbial community composition,which were positively related to soil total N and available phosphorus(P)contents.The abundance of ammonia-oxidizing archaea(AOA)significantly decreased after N addition,whereas ammonia-oxidizing bacteria(AOB)increased in N360 treatment.Compared with low-N group(N0 and N135),the high-N group(N225 and N360)shaped more complex microbial webs and thus improved the stability of the microbial community.Partial least squares path modeling further revealed that N fertilizer had a higher effect on microbial network complexity in the high-N group(0.83)than the low-N group(0.49).Although there were more positive links across all microbial networks,the proportion of negative links significantly increased in the high-N network,suggesting that excess N addition aggravated the competition among microbial species.Disentangling these interactions between microbial communities and N fertilization advances our understanding of biogeochemical processes in paddy soils and their effects on nutrient supply to rice production.Our findings highlighted that highly N-enriched paddy soils have more stable microbial networks and can better sustain soil ecological functions to cope with the ongoing environmental changes.

Unveiling the interaction mechanisms of key functional microorganisms in the partial denitrification-anammox process induced by COD

Partial denitrification-anammox(PD-anammox)is an innovative process to remove nitrate(NO_(3)^(–)–N)and ammonia(NH4+–N)simultaneously from wastewater.Stable operation of the PD-anammox process relies on the synergy and competition between anammox bacteria and denitrifiers.However,the mechanism of metabolic between the functional bacteria in the PD-anammox system remains unclear,especially in the treatment of high-strength wastewater.The kinetics of nitrite(NO_(2)^–N)accumulation during denitrification was investigated using the Michaelis-Menten equation,and it was found that low concentrations of NO_(3)^–N had a more significant effect on the accumulation of NO_(2)^–N during denitrification.Organic matter was a key factor to regulate the synergy of anammox and denitrification,and altered the nitrogen removal pathways.The competition for NO_(2)^–N caused by high COD concentration was a crucial factor that affecting the system stability.Illumina sequencing techniques demonstrated that excess organic matter promoted the relative abundance of the Denitratesoma genus and the nitrite reductase gene nirS,causing the denitrifying bacteria Denitratisoma to compete with Cadidatus Kuenenia for NO_(2)^–N,thereby affecting the stability of the system.Synergistic carbon and nitrogen removal between partial denitrifiers and anammox bacteria can be effectively achieved by controlling the COD and COD/NO_(3)^(–)N.

Salinity causes differences in stratigraphic methane sources and sinks

Methane metabolism,driven by methanogenic and methanotrophic microorganisms,plays a pivotal role in the carbon cycle.As seawater intrusion and soil salinization rise due to global environmental shifts,understanding how salinity affects methane emissions,especially in deep strata,becomes imperative.Yet,insights into stratigraphic methane release under varying salinity conditions remain sparse.Here we investigate the effects of salinity on methane metabolism across terrestrial and coastal strata(15-40 m depth)through in situ and microcosm simulation studies.Coastal strata,exhibiting a salinity level five times greater than terrestrial strata,manifested a 12.05%decrease in total methane production,but a staggering 687.34%surge in methane oxidation,culminating in 146.31%diminished methane emissions.Salinity emerged as a significant factor shaping the methane-metabolizing microbial community's dynamics,impacting the methanogenic archaeal,methanotrophic archaeal,and methanotrophic bacterial communities by 16.53%,27.25%,and 22.94%,respectively.Furthermore,microbial interactions influenced strata system methane metabolism.Metabolic pathway analyses suggested Atribacteria JS1's potential role in organic matter decomposition,facilitating methane production via Methanofastidiosales.This study thus offers a comprehensive lens to comprehend stratigraphic methane emission dynamics and the overarching factors modulating them.

Contrasting response of rice rhizosphere microbiomes to in situ cadmium-contaminated soil remediation

Changes in soil properties and microbial communities regulated rhizosphere protistan assemblages. • Bacterial community was more sensitive to soil amendments than protists and fungi. • Soil amendments trigger the role of specific protistan taxa Cercozoa on microbial interactions. Understanding the responses of different rhizosphere microbial lineages to soil amendments during in situ remediation of Cd-contaminated soil is of great importance in the assessment of the restoration and crop health. Here, we evaluated the effects of lime (LM), biochar (BC), pig manure (PM), and a commercial Mg-Ca-Si conditioner (CMC) on the rice rhizosphere soil physicochemical properties and community assembly of bacteria, fungi, and protists in a six-year consecutive application of soil amendments field trial. Our results indicated that among the four amendments, the BC and CMC had the best efficiency in increasing soil pH, which were 5.2% and 16.2%, respectively. Despite the differences in soil Cd concentrations is not noticeable, all the soil amendment treatments significantly decreased the proportion of available Cd in total Cd compared to the control. Soil amendments significantly altered the diversity of bacterial community, while they had no effect on fungal and protistan communities. Linear discriminant analysis effect size (LEfSe) showed that the bacteria was more sensitive to soil amendment-induced changes. For protists, treatments with LM and BC changed the groups of protistan consumers, while treatments with PM and CMC significantly increased the relative abundances of protistan phototrophs. Co-occurrence network analysis revealed that soil amendments increased microbial network complexity and triggered the role of protists, especially for the predatory protists Cercozoa, on microbial trophic interactions. Further variation partitioning analysis revealed that edaphic properties, bacterial and fungal communities compositions together explained the 77% of the total variation in protistan community, and the stronger correlations between diversity of bacterial and protistan communities suggested that the bacteria community was a more important biotic driver of the protistan community. Overall, our findings demonstrate the distinct responses of rice rhizosphere microbial communities to soil amendment applications, highlighting the interactive associations between microbiomes, which is vital for enhancing our ability to develop effective strategies for sustainable soil management. This study enhances our understanding of the ecological roles of protists under soil amendment applications and highlights their potential contributions in bioremediation and environmental applications for Cd-contaminated soil.

Mechanisms of probiotic Bacillus against enteric bacterial infections

Gastrointestinal infection is a leading cause of gut diseases attracting global health concerns.The emerging antimicrobial resistance in enteric pathogens drives the search of viable and renewable alternatives to antibiotics for the health of both human beings and animals.Spore-forming probiotic Bacillus have received extensively interests for their multiple health benefits,including the restoration of microbiota dysbiosis and the reduction of drug-resistant pathogens.These promising benefits are mainly attributed to the activity of structurally diverse Bacillus-derived metabolites,such as antibacterial compounds,short-chain fatty acids,and other small molecules.Such metabolites show the capacity to directly target either the individual or community of bacterial pathogens,and to potentiate both host cells and gut microbiota.The better understanding of the mechanisms by which probiotic Bacillus and the metabolites modulate the metabolism of hosts and microbiota will advance the screening and development of probiotic Bacillus.In this review,we discuss the interaction among probiotic Bacillus,microbiota and host,and summarize the Bacillus-derived metabolites that act as key players in such interactions,shedding light on the mechanistic understanding of probiotic Bacillus against enteric bacterial infections.

Biochar amendments and its impact on soil biota for sustainable agriculture

Beneficial microbes in soil biota are known to enhance plant growth by stimulating the nutrient supply and by devising certain mechanisms to cope up with the biotic(diseases)or abiotic(salinity,drought,and pollution)stresses.Owing to their effectiveness and sustainability concerns,the application of microbes in the agricultural sector has seen a positive surge recently.Biochar has been commended as an exemplary carrier material for beneficial microbes in the soil ecosystem.Biochar is generally produced from the waste biomasses,which not only resolve the management crisis of agricultural wastes but also render many benefits such as enhancement of soil properties,alteration of nutritional dynamics,removal of pollutants,and in the stimulation of beneficial microbial diversity in soil.The strategic application of biochar in agricultural land could help provide agronomic,economic,and environmental benefits.Since certain risks are associated with the application of biochar,attention needs to be paid while preferring for soil amendments.This present review focused on highlighting the role of microbes in plant growth.The influence of biochar on soil biota along with its detailed mechanisms was discussed further to delineate the scope of biochar in soil amendments.Further,the risks associated with the biochar amendments and the future perspectives in this research arena were highlighted.

Recent developments of lactic acid bacteria and their metabolites on foodborne pathogens and spoilage bacteria:Facts and gaps

Lactic acid bacteria(LAB)are common microorganisms found in various ecosystems including in plants,fermented foods,and the human body.Exploring the biodiversity of lactic acid microflora and characterization of LAB is a new approach to form a variety of starter communities to create innovative nutritional food matrices.There has been growing interest in LAB isolated from non-dairy environments as these bacteria exhibit significant metabolic diversity and have unique taste-forming activities.Disease may be prevented,or treated by LAB but the treatment of disease conditions with LAB is highly dependent on the host's microbiome and diet and varies in both effectiveness and side effects from individual to individual.Future perspectives on the study of LAB may be related to the expansion of our knowledge in the fields of genetics and genetic engineering.The application of genetic science may help to improve existing strains and develop new strains with characteristics designed for specific purposes.Therefore,the preservative effects of LAB and their metabolites,as well as their interaction on the growth of food borne pathogens and food spoilage microorganisms were elucidated.In addition,the competitive models for microbial growth between LAB and other microorganisms as well as the role of LAB in the elimination of toxic compounds in food products were discussed.Moreover,the review provided an overview of the risks and benefits of using LAB in the food industry.

Recent advances in droplet microfluidics for microbiology

Advances in microbiology rely on innovations in technology. Droplet microfluidics, as a versatile and powerful technique that allows high-throughput generation and manipulation of subnanoliter volume droplets, has become an indispensable tool shifting experimental paradigms in microbiology. Droplet microfluidics has opened new avenues to various microbiological research, from resolving single-cell heterogeneity to investigating spatiotemporal dynamics of microbial communities, from precise quantitation of microbiota to systematic decipherment of microbial interactions, and from isolating rare and uncultured microbes to improving genetic engineered strains. In this review, we present recent advances of droplet microfluidics in various fields of microbiology: i) microbial cultivation, ii) microorganism detection and characterization, iii) antibiotic susceptibility testing, iv) microbial interactions, v) microbial biotechnology.We also provide our perspectives on the challenges and future directions for droplet microfluidic-based microbiology research.

Distinct co‑occurrence patterns and driving forces of abundant and rare bacterial communities in the multispecies solid‑state fermentation process of cereal vinegar

Multispecies solid-state fermentation is a traditional processing technique for the traditional Chinese food,such as cereal vinegar,Baijiu,etc.Generally,few abundant and many rare microbes were involved in such processes,and the necessity and roles of the latter are less studied.Here the co-occurrence patterns of abundant and rare bacterial community and abiotic factors infuencing their community assembly were investigated in acetic acid fermentation following starter inoculation,using Zhenjiang aromatic vinegar as a model system.Abundant taxa that contribute to the function of accumulating acid exhibited a ubiquitous distribution while the distribution of rare taxa along the fermentation process unraveled.The species composition of the rare taxa signifcantly altered,but abundant taxa were maintained after inoculation.Moreover,the diversity of rare taxa changed more signifcantly than that of abundant taxa.Both abundant and rare sub-communities,which were contributed more with species turnover than species richness,were demonstrated to be driven by pH,acetic acid,ammonium nitrogen,and ethanol.Stochastic processes regulated the assembly of both sub-communities,but more prominent on rare sub-communities.Co-occurrence network was more governed by rare sub-communities,and the co-variations between microbial communities were predominantly positive,implying that rare taxa played more important role in the fermentation stability and network robustness.Furthermore,seven network connectors were identifed,and three of them belonged to rare taxa.These microbes of diferent modules were enriched at particular phases of fermentation.These results demonstrate the ecological signifcance of rare bacteria and provide new insights into understanding the abiotic factors infuence microbial structure in traditional fermented foods.