FEMS microbiology ecology最新文献

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.

Soil microbial communities play a pivotal role in salt marsh ecosystem functioning, driving processes such as organic matter decomposition and greenhouse gas cycling. Despite their importance, it remains unclear how climate warming will affect the diversity and activity of salt marsh soil microbial communities, limiting our ability to predict the fate of the vast stores of soil organic carbon in these so-called blue carbon ecosystems. Here, we leveraged the Marsh Ecosystem Response to Increased Temperature (MERIT) experiment to investigate the effects of sustained warming on the structure and function of the putatively active microbial community, as assessed by rRNA transcripts, alongside measurements of exo-enzymatic activities involved in carbon and nitrogen acquisition. Our results reveal that, after 5 years of experimental warming by +1.5°C and +3.0°C, the overall structure of the active microbial community remains remarkably stable, suggesting a high degree of resilience to elevated temperatures in this dynamic environment. However, warming selectively promoted drought-tolerant phyla, particularly Actinobacteriota and Firmicutes, which are known for their ability to degrade complex organic compounds and withstand desiccation. These findings suggest that while the active microbial community is broadly resistant to warming, subtle compositional shifts may enhance decomposition of recalcitrant soil carbon.

Marine surface waters contain complex mixtures of chemicals that can adversely affect microzooplankton. There is a lack of toxicity data for this organism group, and we used two different methodologies to fill this gap. We tested the toxicity of three chemical mixtures of polar organic chemicals extracted from marine surface water, using a component-based and a whole-mixture approach. The component-based approach estimates cumulative toxic units for each mixture based on concentrations of individual compounds. The observed hazard data for zooplankton was supplemented with ECOSAR-generated QSAR daphnid LC50s when observed data was missing. ECOSAR performance was evaluated for zooplankton, where 65% of the observed hazard data for zooplankton was predicted within a factor of 10. This approach suggested that none of the mixtures should be toxic to zooplankton at their respective measured environmental concentrations. We found contrasting results using the whole-mixture approach with a reduction in ciliates and dinoflagellates, and change in microzooplankton diversity, at the measured environmental concentrations. We suggest an assessment factor of at least 1000 when using additive toxic units in a component-based risk assessment approach to cover for the extrapolation from acute to chronic toxicity data and for the range of sensitivities among microzooplankton species.

The significant advancements in understanding the roles of anaerobic fungi (AF) within microbial ecology have opened numerous avenues for biotechnological exploitation, particularly in enhancing the productivity of livestock. The efficient, unique, and complex enzyme systems of AF play a determining role in the metabolic conversion of lignocellulosic plant matter into animal products, such as milk and meat by mammalian herbivores. Mitigation of methane emissions through microbial or dietary strategies in ruminants is a major environmental climate change issue. In turn, controlled management of the interkingdom syntrophic interactions among the eukaryotic AF, prokaryotic bacteria, and archaea can lead to the production of valuable biofuels, (biomethane, biohydrogen, and bioethanol), and organic acids. These products can also serve as building blocks in numerous processes to generate high value chemicals in circular bioeconomy.

The rhizosphere microbiome critically determines plant health and productivity. This study investigated the impact of Bacillus subtilis H38 on the taxonomic and functional profiles of the winter wheat (Triticum aestivum L.) rhizosphere microbiome under typical chernozem conditions using 16S rRNA gene sequencing and shotgun metagenomics, complemented by plant phenotypic evaluation and targeted metabolite analysis. Inoculation with B. subtilis H38 significantly restructured the rhizosphere bacterial community, increasing alpha-diversity (Shannon index from 5.8 to 6.7) and showing distinct clustering in beta-diversity analysis. The relative abundance of putative plant-beneficial genera, including Bacillus, Pseudomonas, Azotobacter, and Streptomyces, was significantly elevated. Shotgun metagenomic analysis revealed enrichment of functional genes associated with nitrogen fixation, phosphorus mobilization, phytohormone biosynthesis, siderophore production, and synthesis of antimicrobial compounds. Targeted metabolomic analysis confirmed elevated levels of indole-3-acetic acid (IAA) and key siderophores. Concurrently, treated wheat plants exhibited an 18.0% increase in aboveground biomass and a 25.0% increase in root length under field conditions. These findings underscore the potential of B. subtilis to beneficially reshape the rhizosphere microbiome and its metagenome, leading to enhanced plant growth, and highlight its utility as a potent biofertilizer for improving wheat productivity. This research reinforces the potential of harnessing beneficial plant-microbe interactions to enhance agricultural productivity while minimizing dependence on synthetic agrochemicals.

Zygnematophycean "glacier algae" form extensive blooms on ablating glacier surfaces despite the ultra-oligotrophic conditions apparent. Previous work has postulated that this oligotrophic bloom paradox is due to (i) lower nutrient requirements of glacier algae, (ii) efficient uptake and storage of the nutrients available, and/or (iii) ineffective characterisation of the actual nutrient environment that glacier algae experience. We investigate the latter here by directly sampling the thin (∼2 mm) melt water film in which glacier algal cells reside across three glaciers in Svalbard during the 2023 melt season, comparing to outcomes from more typical bulk ice sampling techniques. Micromelt samples generally contained increased concentrations of ammonium (NH4+), nitrate (NO3-), nitrite (NO2-), and phosphate (PO43-), though trends were not uniform, and concentrations remained well within oligotrophic levels. Several major ion species were significantly increased in micromelt fractions as compared to bulk samples, indicating aeolian deposition and marine aerosol influences on the glacier algal environment. In turn, enhanced micromelt dissolved organic carbon concentrations (DOC) indicated likely DOC delivery by glacier algae to the microbial food web from the onset of bloom formation. Taken together, datasets reveal new fine-scale heterogeneity in the glacier algal meltwater environment.