FEMS microbiology ecology最新文献

A key question in microbial ecology is how the microbiota regulates host invasion by pathogens. Several ecological theories link the diversity, abundance and assembly processes of the microbiota with its resistance to invasion, but the specific properties of microbial communities that confer protection to the host are poorly understood. We addressed this question for the oomycete Plasmopara viticola, the causal agent of grapevine downy mildew. Using state-of-the-art microbial ecology methods, we compared microbial communities associated with asymptomatic and symptomatic leaf tissues to elucidate pathogen-microbiota interactions. Despite visible symptoms, P. viticola infection induced only subtle changes in microbial community composition. Symptomatic tissues showed enrichment in basidiomycete yeasts and Bacillus species, both known for their biocontrol activity, and exhibited a higher degree of determinism in community assembly processes. Asymptomatic tissues hosted more diverse microbiota, but lacked consistent associations with known biocontrol agents. Instead, they were often associated with other airborne grapevine pathogens. These findings suggest a novel interaction scenario: upon infection, P. viticola reshapes locally the leaf microbiota, excluding other pathogens and selecting for beneficial microbes. Although further studies are needed to uncover the underlying mechanisms, these findings underscore the relevance of targeting disease lesions in the search for protective microbial consortia.

Extreme rainfall and flooding are expected to increase in Northern subboreal habitats, altering soil hydrology and impacting greenhouse gas (GHG) fluxes by shifting redox potential and microbial communities as soils transition from aerobic to anaerobic conditions. This study examined the effects of a 2-week growing-season flash flood on bacterial, archaeal, and fungal communities and microbial processes driving CH4 and N2O fluxes in riparian alder (Alnus incana) forests. Flooding reduced soil nitrate accumulation as determined by quantitative polymerase chain reaction and promoted dinitrogen-fixing, nifH gene-carrying bacteria like Geomonas. Sequencing data showed that anaerobic bacteria (Oleiharenicola, Pelotalea) increased during the flood, while N2O emissions declined, indicating a shift towards complete denitrification to N2. However, drier patches within the flooded area emitted N2O, suggesting nitrification or incomplete denitrification. A diverse arbuscular mycorrhizal community was detected, including genera Acaulospora, Archaeospora, Claroideoglomus, Diversispora, and Paraglomus. Flooding increased the abundance of the fungal genera Naucoria, Russula, and Tomentella and the family Thelephoraceae, which symbiotically support alder trees in nitrogen uptake and carbon sequestration. Microtopographic differences of 0.3-0.7 m created spatial variability in GHG emissions during flooding, with some waterlogged areas emitting CH4, while others enhanced CH4 oxidation (determined by FAPROTAX) and promoted nitrification-driven N2O emissions in drier, elevated zones. We conclude that flash flooding during the active growing season significantly affects nitrogen-fixing and nitrifying microbes and alters symbiotic fungal community composition, creating spatial variability in GHG emissions.

Rice is a staple crop relevant to present and future human feeding. However, these agroecosystems significantly contribute to greenhouse gas methane emissions. In Uruguay, a traditional low-intensity, reduced-tillage rice system alternates annual rice crops with pastures for livestock. We hypothesize that rice crop intensification impacts aerobic methanotrophic communities associated with rice roots, which are crucial in mitigating methane emissions. The pmoA gene abundance, methane oxidation potential (MOP), and methanotrophic community composition by 16S rRNA gene Illumina MiSeq (V4 region) allowed us to determine the dynamics of these communities in bulk and rhizospheric soils from continuous rice (CR) and rice-pastures (RP) rotations throughout the crop cycle. Results showed that rice crop intensification significantly affected MOP and pmoA abundance in both compartments. The tillering stage showed the greatest pmoA abundance and MOP. Rhizospheric methanotrophic communities from the CR and RP systems at flowering differed greatly. While Methylocystis dominated rhizospheric CR soil, Methylocella predominated in those from RP rotation. Active rhizospheric methanotrophic communities at flowering detected by 13CH4 DNA-SIP were dominated by distinct Methylocystis-affiliated ASVs in both cropping systems. However, other active genera were differentially enriched in the two contrasting cropping systems. These results suggest aerobic methanotrophs could be a microbial guild sensitive to crop intensification.

Saccharomyces cerevisiae is occasionally infected by dsRNA totiviruses and their toxin-encoding dsRNA satellite nucleic acids. The autonomous totivirus and its satellite can coexist but with an asymmetric dependence of the satellite on the totivirus for replication and maintenance inside the host cell. Satellites provide their yeast hosts with inhibitory toxins and the necessary self-immunity; loss of the satellite equates to loss of toxin immunity. Because these viral elements lack known extracellular stages, and sex is suspected to be rare, they are assumed to be transmitted vertically, implying that infection states should correlate with host genotypes. However, totivirus-satellite coinfections are rarely examined in natural populations, leaving their associations with host genotypes poorly understood. We screened a multiyear, vineyard-associated population of S. cerevisiae isolates from New Zealand to examine the stability of host-virus associations over time, both within and across genotypes. Over half of the wild isolates harbored infections (55%), but less than half of these (37% of infected) had toxin-encoding satellites. Genotypes that persisted across years typically maintained consistent infection states. However, we also observed stepwise transitions from coinfection through infection to an infection-free state, as well as acquisition of totiviruses and satellites. Genotypes clustered strongly by infection state, and population heterozygosity was significantly lower than expected, supporting vertical transmission while suggesting that outcrossing is not responsible for the acquisition of higher infection states. Despite occasional intragenotypic transitions, genotype clustering by infection state remained intact, suggesting that such transitions are transient and that host genotypes may have optimal infection states with regard to totiviruses and their satellites.

Both deterministic (e.g. species-environment interactions) and stochastic processes (e.g. random birth and death events) shape communities, but it remains poorly understood, which environmental conditions promote stochasticity. Here, we investigated interactive effects of nutrient availability and community size on stochasticity in order to predict how eutrophication and biomass loss shift the balance between predictable and random community dynamics. For this, we used freshwater bacterial communities in a microcosm experiment, where communities were diluted to varying sizes and exposed to low, intermediate, and high nutrient concentrations. Stochasticity was estimated with null modelling and as beta-diversity among replicate communities. At low nutrient concentrations, deterministic processes dominated, especially in smaller communities, which had the lowest diversity and abundance. Whereas, higher nutrient concentrations increased stochasticity. In contrast to theoretical predictions, this was particularly the case in larger communities with the highest diversity and abundance, likely due to stochastic initial growth. The findings underline how nutrient availability and community size jointly influence stochastic assembly processes, with important consequences for bacterial diversity and ecosystem functioning under environmental change.

The production of fuel ethanol in sugarcane biorefineries is a nonaseptic industrial operation, which employs cell recycling and the use of adapted Saccharomyces cerevisiae strains. Microbial contaminants are present and, depending on the conditions, may lead to process performance deterioration. Past studies have identified the main microbial species present in this environment, using culture-dependent techniques. A few recent studies started to deploy culture-independent techniques to better understand this microbiota and its dynamics. In both cases, lactic acid bacteria have been identified as the main contaminating microorganisms. Less than a handful of reports are available on the interactions between yeast and contaminating bacteria, using synthetic microbial communities, proposing that interactions are not necessarily always detrimental. The present mini-review aims at systematizing the current knowledge on the microbiota present in the alcoholic fermentation environment in sugarcane biorefineries and setting the ground and claiming the need for a microbial ecology perspective to be applied to this system, which in turn might lead to future process improvements.

Microplastics (MPs) frequently co-occur with pesticides and veterinary medicines in agricultural soils. However, their interactive effects on soil microbiota remain largely unknown. Therefore, we investigated the effects of three MP types (LDPE-, PBAT-, and starch-based), applied at two concentrations (0.01% and 0.1%), either alone or in combination with the fungicide pyraclostrobin and/or the anthelminthic albendazole (ABZ), on soil microbial functioning. Nitrate levels, nitrification rates, ammonia-oxidizing microorganisms, and denitrifying bacteria served as indicators of perturbations on soil N cycling in soils from France, the Netherlands, and Greece. Microbial responses were soil-dependent, with the Greek soil being the most affected. In contrast, plastic type- and dose-dependent effects were sporadic and limited in the French and Dutch soil. In the Greek soil, all MP types increased the abundance of ammonia-oxidizing bacteria and nitrification rates, accompanied by a compensatory decline in ammonia-oxidizing archaea and commamox bacteria. These effects were reversed by the co-application of MPs with ABZ. On the other hand, denitrifying bacteria remained unaffected in all soils. Our results are alarming, considering the perturbation of nitrification imposed by MPs and other soil pollutants, which could enhance greenhouse gas emissions or adversely affect soil fertility and agricultural production.

The aim was to assess the effect of straw biochar on microbiomes along the depth (30-80 cm) of two coarse sandy subsoils. We hypothesized that biochar modifies extracellular enzyme activities (EEA), and diversity and structure of microbiomes across the subsoil depths. Two subsoils were amended with straw biochar (0%-4% w/w) and incubated for 16 months in a column experiment with two cultivations of spring barley. EEA were assessed using fluorogenic assays, while the prokaryotic and fungal communities were analyzed via 16S rRNA gene and ITS2 amplicon sequencing, respectively. Biochar significantly increased water holding capacity and pH. It also significantly decreased the phosphomonoesterase activity, suggesting enhanced soil phosphate bioavailability. In both subsoils, biochar significantly increased the prokaryotic α-diversity index. Biochar impacted prokaryotic community structures more than fungal community structures. Prokaryotic community structures were significantly different with increasing biochar content at deeper soil depths. Moreover, in both subsoils, biochar significantly increased the relative abundance of a prokaryotic consortium. We conclude that the biochar-induced improvements in physicochemical soil properties stimulate microbial diversity and functional activity across varying depths in coarse sandy subsoils. These findings are valuable for assessing the potential benefits of biochar application on agricultural subsoil health.

Understanding the initial formation and development of lichens is crucial for elucidating the mechanisms behind the formation of complex lichen thalli and their maintenance in long-term symbioses. These symbiotic relationships provide significant ecological advantages for both partners, expanding their ecological niches and allowing them, in many cases, to overcome extreme environmental conditions. The correct development of thalli likely relies on the selection of suitable photobionts from the environment. In this study, we focused on the impact of lichen age on the overall diversity of photobiont partners and examined how mycobiont preference toward their symbionts changes at different developmental stages. Using the lichen Protoparmeliopsis muralis as a model organism, we observed a strong correlation between the diversity of photobionts and lichen age, confirmed by both molecular data and morphological observations. Our findings indicate greater photobiont diversity in older thalli, suggesting that lichens retain the majority of algae they collect throughout their lifespan, potentially as an adaptation to changing environmental conditions. Additionally, we found that some lichen samples contained only low levels of Trebouxia algae, indicating that P. muralis does not consistently rely on this typical partner and that local environmental conditions may significantly influence its symbiotic composition.