Prevalent emergence of reciprocity among cross-feeding bacteria

Microbial Biotic Associations Dominated Adaptability Differences of Dioecious Poplar Under Salt Stress

How different stress responses by male and female plants are influenced by interactions with rhizosphere microbes remains unclear. In this study, we employed poplar as a dioecious model plant and quantified biotic associations between microorganisms to explore the relationship between microbial associations and plant adaptation. We propose a health index (HI) to comprehensively characterize the physiological characteristics and adaptive capacity of plants under stress. It was found that male poplars demonstrated higher salt stress tolerance than females, and root-secreted citric acid was significantly higher in the rhizospheres of male poplars. Positive biotic association among bacteria increased poplar HI significantly under salt stress, while fungal and cross-domain biotic association (bacteria-fungi) did not. We further identified a keystone bacterial taxon regulating bacterial biotic association, ASV_22706, which was itself regulated by citric acid and significantly positively correlated with host HI. The abundance of keystone fungal taxa was positively correlated with HI of male poplars and negatively correlated with HI of female poplars. Compared with female poplars, male poplars enriched more prebiotics and probiotics under stress. This work primarily reveals the relationship between adaptation differences and microbial interactions in dioecious plants, which suggests a microbial approach to improve plant adaptability to stress conditions.

Branched-chain amino acid metabolism supports Roseobacteraceae positive interactions in marine biofilms

Interspecies interactions are key factors affecting the stability of microbial communities. However, microbial interactions in marine biofilms, which constitute up to 80% of the microbial biomass in certain marine environments, are not well understood. We addressed this knowledge gap by coculturing four marine biofilm-derived Roseobacteraceae strains (Leisingera aquaemixtae M597, Roseibium aggregatum S1616, Alloyangia pacifica T6124, and Sulfitobacter indolifex W002) in 14 single carbon sources. Overall, 140 coculture experiments revealed 39.3% positive interactions compared to 8.3% negative interactions. When the carbon source was consumed by only one strain, the interaction between the strains was more likely to be positive. The interaction between S1616 and M597, when cultured in D-gluconic acid, was further studied as an example. S1616-M597 coculture displayed a higher D-gluconic acid consumption rate than S1616 monoculture, whereas M597 could not use D-gluconic acid as the sole carbon source. The supernatant of S1616 monoculture supported the growth of M597, and branched-chain amino acids in the supernatant were consumed. Transcriptomic analysis suggested that M597 induced the expression of genes for branched-chain amino acid biosynthesis in S1616. Additionally, metagenomic analysis revealed the wide distribution and a strongly correlated co-occurrence of the four strains in global oceanic biofilms. Together, our findings show that interspecies positive interactions are prevalent among marine-biofilm Roseobacteraceae, and the interactions are likely to be mediated by branched-chain amino acids metabolism.

IMPORTANCE

Interspecies interactions are crucial for microbial community structure and function. Despite well-studied social behaviors in model microorganisms, species interactions in natural marine biofilms especially Roseobacteraceae with complex metabolic pathways are not well understood. Our findings suggest that positive microbial interactions, which can be mediated by branched-chain amino acid biosynthesis, are common among marine-biofilm Roseobacteraceae. This study provides new insights into microbial interactions and the ecology of marine biofilms.

Unveiling the hidden world: How arbuscular mycorrhizal fungi and its regulated core fungi modify the composition and metabolism of soybean rhizosphere microbiome

BACKGROUND

The symbiosis between arbuscular mycorrhizal fungi (AMF) and plants often stimulates plant growth, increases agricultural yield, reduces costs, thereby providing significant economic benefits. AMF can also benefit plants through affecting the rhizosphere microbial community, but the underlying mechanisms remain unclear. Using Rhizophagus intraradices as a model AMF species, we assessed how AMF influences the bacterial composition and functional diversity through 16 S rRNA gene sequencing and non-targeted metabolomics analysis in the rhizosphere of aluminum-sensitive soybean that were inoculated with pathogenic fungus Nigrospora oryzae and phosphorus-solubilizing fungus Talaromyces verruculosus in an acidic soil.

RESULTS

The inoculation of R. intraradices, N. oryzae and T. verruculosus didn't have a significant influence on the levels of soil C, N, and P, or various plant characteristics such as seed weight, crude fat and protein content. However, their inoculation affected the structure, function and nutrient dynamics of the resident bacterial community. The co-inoculation of T. verruculosus and R. intraradices increased the relative abundance of Pseudomonas psychrotolerans, which was capable of N-fixing and was related to cry-for-help theory (plants signal for beneficial microbes when under stress), within the rhizosphere. R. intraradices increased the expression of metabolic pathways associated with the synthesis of unsaturated fatty acids, which was known to enhance plant resistance under adverse environmental conditions. The inoculation of N. oryzae stimulated the stress response inside the soil environment by enriching the polyene macrolide antifungal antibiotic-producing bacterial genus Streptomyces in the root endosphere and upregulating two antibacterial activity metabolic pathways associated with steroid biosynthesis pathways in the rhizosphere. Although inoculation of pathogenic fungus N. oryzae enriched Bradyrhizobium and increased soil urease activity, it had no significant effects on biomass and N content of soybean. Lastly, the host niches exhibited differences in the composition of the bacterial community, with most N-fixing bacteria accumulating in the endosphere and Rhizobium vallis only detected in the endosphere.

CONCLUSIONS

Our findings demonstrate that intricate interactions between AMF, associated core fungi, and the soybean root-associated ecological niches co-mediate the regulation of soybean growth, the dynamics of rhizosphere soil nutrients, and the composition, function, and metabolisms of the root-associated microbiome in an acidic soil.

Community interactions among microbes give rise to host-microbiome mutualisms in an aquatic plant

Microbiomes often benefit plants, conferring resistance to pathogens, improving stress tolerance, or promoting plant growth. As potential plant mutualists, however, microbiomes are not a single organism but a community of species with complex interactions among microbial taxa and between microbes and their shared host. The nature of ecological interactions among microbes in the microbiome can have important consequences for the net effects of microbiomes on hosts. Here, we compared the effects of individual microbial strains and 10-strain synthetic communities on microbial productivity and host growth using the common duckweed Lemna minor and a synthetic, simplified version of its native microbiome. Except for Pseudomonas protegens, which was a mutualist when tested alone, all of the single strains we tested were commensals on hosts, benefiting from plant presence but not increasing host growth relative to uninoculated controls. However, 10-strain synthetic microbial communities increased both microbial productivity and duckweed growth more than the average single-strain inoculation and uninoculated controls, meaning that host-microbiome mutualisms can emerge from community interactions among microbes on hosts. The effects of community inoculation were sub-additive, suggesting at least some competition among microbes in the duckweed microbiome. We also investigated the relationship between L. minor fitness and that of its microbes, providing some of the first empirical estimates of broad fitness alignment between plants and members of their microbiomes; hosts grew faster with more productive microbes or microbiomes.

IMPORTANCE

There is currently substantial interest in engineering synthetic microbiomes for health or agricultural applications. One key question is how multi-strain microbial communities differ from single microbial strains in their productivity and effects on hosts. We tested 20 single bacterial strains and 2 distinct 10-strain synthetic communities on plant hosts and found that 10-strain communities led to faster host growth and greater microbial productivity than the average, but not the best, single strain. Furthermore, the microbial strains or communities that achieved the greatest cell densities were also the most beneficial to their hosts, showing that both specific single strains and multi-strain synthetic communities can engage in high-quality mutualisms with their hosts. Our results suggest that ~5% of single strains, as well as multi-strain synthetic communities comprised largely of commensal microbes, can benefit hosts and result in effective host-microbe mutualisms.

Interspecies interactions in dairy biofilms drive community structure and response against cleaning and disinfection

Interspecies interactions within a biofilm community influence population dynamics and community structure, which in turn may affect the bacterial stress response to antimicrobials. This study was conducted to assess the impact of interactions between Kocuria salsicia and a three-species biofilm community (comprising Stenotrophomonas rhizophila, Bacillus licheniformis, and Microbacterium lacticum) on biofilm mass, the abundance of individual species, and their survival under a laboratory-scale cleaning and disinfection (C&D) regime. The presence of K. salsicia enhanced the cell numbers of all three species in pairwise interactions. The outcomes derived from summing up pairwise interactions did not accurately predict the bacterial population dynamics within communities of more than two species. In four-species biofilms, we observed the dominance of S. rhizophila and B. licheniformis, alongside a concurrent reduction in the cell counts of K. salsicia and M. lacticum. This pattern suggests that the underlying interactions are not purely non-transitive; instead, a more complex interplay results in the dominance of specific species. We observed that bacterial spatial organization and matrix production in different mixed-species combinations affected survival in response to C&D. Confocal microscopy analysis of spatial organization showed that S. rhizophila localized on the biofilm formed by B. licheniformis and M. lacticum, and S. rhizophila was more susceptible to C&D. Matrix production in B. licheniformis, evidenced by alterations in biofilm mass and by scanning electron microscopy, demonstrated its protective role against C&D, not only for this species itself, but also for neighbouring species. Our findings emphasise that various social interactions within a biofilm community not only affect bacterial population dynamics but also influence the biofilm community's response to C&D stress.

Unveiling the crucial role of soil microorganisms in carbon cycling: A review

Soil microorganisms, by actively participating in the decomposition and transformation of organic matter through diverse metabolic pathways, play a pivotal role in carbon cycling within soil systems and contribute to the stabilization of organic carbon, thereby influencing soil carbon storage and turnover. Investigating the processes, mechanisms, and driving factors of soil microbial carbon cycling is crucial for understanding the functionality of terrestrial carbon sinks and effectively addressing climate change. This review comprehensively discusses the role of soil microorganisms in soil carbon cycling from three perspectives: metabolic pathways, microbial communities, and environmental influences. It elucidates the roles of different microbial species in carbon cycling and highlights the impact of microbial interactions and environmental factors on carbon cycling. Through the synthesis of 2171 relevant papers in the Web of Science Core database, we elucidated the ecological community structure, activity, and assembly mechanisms of soil microorganisms crucial to the soil carbon cycle that have been widely analyzed. The integration of soil microbial carbon cycle and its driving factors are vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change. Such integration is vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change.

Rhizobacterial syntrophy between a helper and a beneficiary promotes tomato plant health

Microbial interactions impact the functioning of microbial communities. However, microbial interactions within host-associated communities remain poorly understood. Here, we report that the beneficiary rhizobacterium Niallia sp. RD1 requires the helper Pseudomonas putida H3 for bacterial growth and beneficial interactions with the plant host. In the absence of the helper H3 strain, the Niallia sp. RD1 strain exhibited weak respiration and elongated cell morphology without forming bacterial colonies. A transposon mutant of H3 in a gene encoding succinate-semialdehyde dehydrogenase displayed much attenuated support of RD1 colony formation. Through the subsequent addition of succinate to the media, we found that succinate serves as a public good that supports RD1 growth. Comparative genome analysis highlighted that RD1 lacked the gene for sufficient succinate, suggesting its evolution as a beneficiary of succinate biosynthesis. The syntrophic interaction between RD1 and H3 efficiently protected tomato plants from bacterial wilt and promoted tomato growth. The addition of succinate to the medium restored complex II-dependent respiration in RD1 and facilitated the cultivation of various bacterial isolates from the rhizosphere. Taken together, we delineate energy auxotrophic beneficiaries ubiquitous in the microbial community, and these beneficiaries could benefit host plants with the aid of helpers in the rhizosphere.

Metabolic exchanges are ubiquitous in natural microbial communities

Microbial communities drive global biogeochemical cycles and shape the health of plants and animals-including humans. Their structure and function are determined by ecological and environmental interactions that govern the assembly, stability and evolution of microbial communities. A widely held view is that antagonistic interactions such as competition predominate in microbial communities and are ecologically more important than synergistic interactions-for example, mutualism or commensalism. Over the past decade, however, a more nuanced picture has emerged, wherein bacteria, archaea and fungi exist within interactive networks in which they exchange essential and non-essential metabolites. These metabolic interactions profoundly impact not only the physiology, ecology and evolution of the strains involved, but are also central to the functioning of many, if not all, microbiomes. Therefore, we advocate for a balanced view of microbiome ecology that encompasses both synergistic and antagonistic interactions as key forces driving the structure and dynamics within microbial communities.

Are Bacteria Leaky? Mechanisms of Metabolite Externalization in Bacterial Cross-Feeding

The metabolism of a bacterial cell stretches beyond its boundaries, often connecting with the metabolism of other cells to form extended metabolic networks that stretch across communities, and even the globe. Among the least intuitive metabolic connections are those involving cross-feeding of canonically intracellular metabolites. How and why are these intracellular metabolites externalized? Are bacteria simply leaky? Here I consider what it means for a bacterium to be leaky, and I review mechanisms of metabolite externalization from the context of cross-feeding. Despite common claims, diffusion of most intracellular metabolites across a membrane is unlikely. Instead, passive and active transporters are likely involved, possibly purging excess metabolites as part of homeostasis. Re-acquisition of metabolites by a producer limits the opportunities for cross-feeding. However, a competitive recipient can stimulate metabolite externalization and initiate a positive-feedback loop of reciprocal cross-feeding.

Salt stress altered anaerobic microbial community and carbon metabolism characteristics: The trade-off between methanogenesis and chain elongation

Discharge of saline organic wastewater is increasing worldwide, yet how salt stress disrupts the microbial community's structure and metabolism in bioreactors has not been systematically investigated. The non-adapted anaerobic granular sludge was inoculated into wastewater with varying salt concentration (ranging from 0% to 5%) to examine the effects of salt stress on the structure and function of the anaerobic microbial community. Result indicated that salt stress had a significant impact on the metabolic function and community structure of the anaerobic granular sludge. Specifically, we observed a notable reduction in methane production in response to all salt stress treatments (r = -0.97, p < 0.01), while an unexpected increase in butyrate production (r = 0.91, p < 0.01) under moderate salt stress (1-3%) with ethanol and acetate as carbon sources. In addition, analysis of microbiome structures and networks demonstrated that as the degree of salt stress increased, the networks exhibited lower connectance and increased compartmentalization. The abundance of interaction partners (methanogenic archaea and syntrophic bacteria) decreased under salt stress. In contrast, the abundance of chain elongation bacteria, specifically Clostridium kluyveri, increased under moderate salt stress (1-3%). As a consequence, the microbial carbon metabolism patterns shifted from cooperative mode (methanogenesis) to independent mode (carbon chain elongation) under moderate salt stress. This study provides evidence that salt stress altered the anaerobic microbial community and carbon metabolism characteristics, and suggests potential guidance for steering the microbiota to promote resource conversion in saline organic wastewater treatment.