Environmental microbiology最新文献

Coastal ecosystems are increasingly exposed to high nutrient loads and salinity intrusions due to rising seawater levels. Microbial communities, key drivers of elemental cycles in these ecosystems, consequently, experience fluctuations. This study investigates how the methane-rich coastal sediment microbiome from the Stockholm Archipelago copes with high and low nitrogen and sulfide loading by simulating coastal conditions in two methane-saturated anoxic brackish bioreactors. Over a year, the bioreactors were subjected to the same ratio of nitrate, ammonium and sulfide (2:1:1) under eutrophic or oligotrophic conditions and monitored using 16S rRNA gene amplicon and metagenomic sequencing. Sulfide was depleted in both conditions. Sulfide-dependent denitrification was the predominant process in eutrophic conditions, whereas dissimilatory nitrate reduction to ammonium dominated under oligotrophic conditions. Methane oxidation was driven by Methylobacter and Methylomonas in eutrophic conditions, whereas a more diverse methane-oxidising microbial community developed under oligotrophic conditions, which likely competed for nitrate with anaerobic methanotrophic archaea and the gammaproteobacterial MBAE14. Novel putative copper-dependent membrane-bound monooxygenases (Cu-MMOs) were identified in MBAE14 and co-enriched Rugosibacter genomes, suggesting the need for further physiological and genetic characterisation. This study highlights the importance of understanding coastal anoxic microbiomes under fluctuating conditions, revealing complex interactions and novel pathways crucial for ecosystem functioning.

Nitrogen compounds often serve as crucial electron donors and acceptors in microbial energy metabolism, playing a key role in biogeochemical cycles. The energetic favorability of nitrogen oxidation–reduction (redox) reactions, driven by the thermodynamic properties of these compounds, may have shaped the evolution of microbial energy metabolism, though the extent of their influence remains unclear. This study quantitatively evaluated the similarity between energetically superior nitrogen reactions, identified from 988 theoretically plausible reactions, and the nitrogen community-level network, reconstructed as a combination of enzymatic reactions representing intracellular to interspecies-level reaction interactions. Our analysis revealed significant link overlap rates between these networks. Notably, composite enzymatic reactions aligned more closely with energetically superior reactions than individual enzymatic reactions. These findings suggest that selective pressure from the energetic favorability of redox reactions can operate primarily at the species or community level, underscoring the critical role of thermodynamics in shaping microbial metabolic networks and ecosystem functioning.

Monooxygenase (MO) enzymes are responsible for the oxidation of hydrocarbons and other compounds in the carbon and nitrogen cycles, are important for the biodegradation of pollutants and can act as biocatalysts for chemical manufacture. The soluble di-iron monooxygenases (SDIMOs) are of interest due to their broad substrate range, high enantioselectivity and ability to oxidise inert substrates such as methane. Here, we re-examine the phylogeny and functions of these enzymes, using recent advances in the field and expansions in sequence diversity in databases to highlight relationships between SDIMOs and revisit their classification. We discuss the impact of horizontal gene transfer on SDIMO phylogeny, the potential of SDIMOs for the biodegradation of pollutants and the importance of heterologous expression as a tool for understanding SDIMO functions and enabling their use as biocatalysts. Our analysis highlights current knowledge gaps, most notably, the unknown substrate ranges and physiological roles of enzymes that have so far only been detected via genome or metagenome sequencing. Enhanced understanding of the diversity and functions of the SDIMO enzymes will enable better prediction and management of biogeochemical processes and also enable new applications of these enzymes for biocatalysis and bioremediation.

Recently, biomass of invertebrates has declined substantially at many locations with the implications of this biodiversity loss for ecosystems yet unknown. Through multitrophic interactions, plant- and soil-associated microbiomes might be altered, causing a cascade of changes on diverse ecosystem processes. We simulated aboveground invertebrate decline in grassland ecosystems with two levels of invertebrate biomass (36% and 100% of current ambient conditions), plus a control with no invertebrates present. Each standardised grassland mesocosm additionally contained one clonal Quercus robur L. sapling to investigate the extent of invertebrate decline effects exceeding grasslands. We investigated oak biomass partitioning and mycorrhiza formation, oak leaf transcriptome and microbiome composition of leaves, roots and rhizosphere. While invertebrate decline did not significantly affect oak performance and herbivory-related gene expression, fungal communities presented an increase of saprotrophs and pathogens, especially in leaves. Among leaf-inhabiting bacteria, Proteobacteria and Actinobacteria increased under invertebrate decline. The belowground microbiome was only little affected. But, invertebrate decline came along with a reduced influence on predators leading to an elevated aphids infestation that proofed able to alter microbiota. Our findings establish a strong difference between above- and belowground, with the impacts of invertebrate decline being more pronounced in the leaf microbiome.

Shallow underwater hydrothermal systems are often overlooked despite their potential contribution to marine diversity and biogeochemistry. Over a decade after its eruption, the Tagoro submarine volcano continues to emit heat, reduced compounds, and nutrients into shallow waters, serving as a model system for studying the effects of diffuse hydrothermal fluids on surface microbial communities. The impact on both phytoplankton and bacterial communities was examined through experimental manipulations mimicking dilution levels up to ~100 m from the primary crater of Tagoro. Chlorophyll a concentration doubled in the presence of hydrothermal products, with peak levels detected about a day earlier than in controls. Picoeukaryotes and Synechococcus cell abundances moderately increased, yet small eukaryotic phytoplankton (≤ 5 μm) predominated in the hydrothermally enriched bottles. Dinoflagellates, diatoms, small green algae and radiolarians particularly benefited from the hydrothermal inputs, along with phototrophic and chemoautotrophic bacteria. Our results indicate that hydrothermal products in shallow waters enhance primary production driven by phototrophic microbes, potentially triggering a secondary response associated with increased organic matter availability. Additionally, protistan grazing and parasitism emerged as key factors modulating local planktonic communities. Our findings highlight the role of shallow submarine hydrothermal systems in enhancing local primary production and element cycling.

Fungus-farming termites cultivate a Termitomyces fungus monoculture in enclosed gardens (combs) free of other fungi, except during colony declines, where Pseudoxylaria spp. stowaway fungi appear and take over combs. Here, we determined Volatile Organic Compounds (VOCs) of healthy Macrotermes bellicosus nests in nature and VOC changes associated with comb decay during Pseudoxylaria takeover. We identified 443 VOCs and unique volatilomes across samples and nest volatilomes that were mainly composed of fungus comb VOCs with termite contributions. Few comb VOCs were linked to chemical changes during decay, but longipinocarvone and longiverbenone were only emitted during comb decay. These terpenes may be involved in Termitomyces defence against antagonistic fungi or in fungus-termite signalling of comb state. Both comb and Pseudoxylaria biomass volatilomes contained many VOCs with antimicrobial activity that may serve in maintaining healthy Termitomyces monocultures or aid in the antagonistic takeover by Pseudoxylaria during colony decline. We further observed a series of oxylipins with known functions in the regulation of fungus germination, growth, and secondary metabolite production. Our volatilome map of the fungus-farming termite symbiosis provides new insights into the chemistry regulating complex interactions and serves as a valuable guide for future work on the roles of VOCs in symbioses.

Horizontal genetic transfer (HGT) is a significant driver of genomic novelty in all domains of life. HGT has been investigated in many studies however, the focus has been on conspicuous protein-coding DNA transfers that often prove to be adaptive in recipient organisms and are therefore fixed longer-term in lineages. These results comprise a subclass of HGTs and do not represent exhaustive (coding and non-coding) DNA transfer and its impact on ecology. Uncovering exhaustive HGT can provide key insights into the connectivity of genomes in communities and how these transfers may occur. In this study, we use the term frequency-inverse document frequency (TF-IDF) technique, that has been used successfully to mine DNA transfers within real and simulated high-quality prokaryote genomes, to search for exhaustive HGTs within an extremophilic microbial community. We establish a pipeline for validating transfers identified using this approach. We find that most DNA transfers are within-domain and involve non-coding DNA. A relatively high proportion of the predicted protein-coding HGTs appear to encode transposase activity, restriction-modification system components, and biofilm formation functions. Our study demonstrates the utility of the TF-IDF approach for HGT detection and provides insights into the mechanisms of recent DNA transfer.