FEMS microbiology ecology最新文献

Nitrate reduction coupled to Fe(II) oxidation (NRFeOx) contributes to Fe cycling in the estuarian sediments of the Río Tinto river (Huelva, Spain). However, it is not yet known (i) whether and which NRFeOx microorganisms can be enriched from the reduced sediment layer and (ii) how in situ pH and salinity fluctuations affect NRFeOx. Therefore, we (i) used two different approaches, such as microcosm experiments (sediment amended with either NO3-/Fe2+aq or acetate/NO3-/Fe2+aq) and enrichment cultures (medium amended with acetate/NO3-/Fe2+aq) to enrich NRFeOx microorganisms to (ii) test their salinity and pH tolerance under simulated high tide and low tide conditions. We found that different microorganisms such as Thiobacillus (up to 9.7 ± 5.8% DNA-based 16S rRNA gene abundance) and Denitromonas (83.6% DNA-based 16S rRNA gene abundance) were contributing to NRFeOx in the microcosm experiments and enrichment culture approach, respectively. The strong buffering capacity of the native sediment and the presence of additional organic carbon as acetate can favor NRFeOx microorganisms during acidic water influx (low tide) events. The ∼100% conversion of NO3- to NO₂- under high tide conditions was observed both in the enrichment cultures and microcosm experiment when acetate was added suggesting the chemodenitrification may be the primary Fe(II) oxidation pathway under salty conditions.

Microbial biomineralization is a key process in natural and anthropogenic environments. Certain bacteria and archaea produce cellular energy via anaerobic respiration using metals and metalloids as terminal electron acceptors, producing intra- and extracellular biominerals. This article explores the biomineralization of arsenic (As), iron (Fe), sulfur (S) and selenium (Se), in relation with microbial respiratory processes. Ferric iron (FeIII) and the oxyanions of As, S and Se are used as terminal electron acceptors by specialized bacteria and archaea, providing significant amounts of energy under anoxic and nutrient-limiting conditions. These transformations result in the formation of various types of arsenic sulfides, iron (oxyhydr)oxides and sulfides, elemental S/S0 and elemental Se/Se0 biominerals, which will be the focus of this review. Certain biominerals (e.g. S0) function as storage compounds; others, like Se0, may increase the density and the buoyancy of bacteria harboring them or are by-products of this process. Arsenic sulfides and iron (oxyhydr)oxides and sulfides appear to be by-product biominerals or have a yet unknown function. The use of these biominerals as biosignatures is an open topic and an ongoing debate. Further exploration of the reviewed biominerals is needed from both fundamental and applied viewpoints, aspects which will be covered in this review.

The addition of conductive materials promotes interactions between bacteria as they facilitate the exchange of reducing equivalents among cells. In this work, the impact of electron conductive compounds (magnetite, activated carbon, or iron salts) was investigated on a Clostridium acetobutylicum/Clostridium carboxidivorans co-culture. Co-culturing both species with soluble iron salts or magnetite significantly improved carbon recovery in liquid end-products (75%-85% of added carbon) compared to control and activated carbon supplementation (50%-55% of added carbon). The addition of magnetite enhanced the production of longer-chain acids and alcohols (C4 and C6) when compared to all other treatments and reached the highest production after 44 h of fermentation. This effect was not observed in C. carboxidivorans nor in C. acetobutylicum pure cultures, advocating for a cooperation between the two species. Among comparisons to the behaviour observed in pure cultures, we suggest magnetite was first used as a sink of reduced equivalents produced by C. carboxidivorans and later as a source of energy for C. acetobutylicum for the production of elongated short-chain fatty acids and alcohols. We propose that adding magnetite (iron) could be an effective strategy to enhance alcohol production in synthetic clostridia consortia.

Freshwater autotrophic biofilms play a vital role in primary production and nutrient cycling in freshwater ecosystems but are increasingly exposed to chemical stressors such as antibiotics or herbicides. Although nutrient availability may modulate biofilm sensitivity, its impact on biofilm responses to these stressors remains poorly understood. In four independent experiments, we investigated the functional (ash-free dry weight and chlorophyll a, b and c) and structural (16S/18S rRNA metabarcoding) responses of stream-derived biofilms under low- and high-nutrient levels to chronic exposure (14 days) to the antibiotic ciprofloxacin and the herbicide propyzamide in laboratory stream microcosms. High-nutrient levels strongly increased biofilms functional responses and altered the community composition. Chemical exposure led to pronounced shifts in prokaryotic (ciprofloxacin) and eukaryotic (propyzamide) communities, but without significant effects on functional responses, suggesting functional redundancy and ecological buffering capacity of freshwater biofilms. These results highlight the critical role of nutrient supply in biofilm responses and the need for caution when extrapolating laboratory results to field conditions.

Unmanaged plastic waste in Sub-Saharan Africa pollutes large areas and degrades into microplastics (MPs). Surfaces of MP are colonized by bacteria and fungi, resulting in the plastisphere. Plastispheres from high population hotspots on the African continent enrich pathogenic fungi, posing a potential threat to human health. Prokaryotes in such plastispheres are unknown to date. Thus, we analysed the prokaryotic microbiome of native plastisphere and soil by 16S rRNA gene amplicon sequencing, with a focus on community assembly mechanisms and putative pathogenic bacteria. A strong plastic-dependent depletion of archaeal ammonia oxidizing Nitrososphaeraceae was observed. Prokaryotic but not archaeal beta diversity significantly differed between plastisphere and soil microbiomes. The prokaryotic pathogenic potential in the plastisphere was marginally increased relative to soil, suggesting that MP is a driver for fungal rather than bacterial pathogens. Null model comparisons revealed a moderately stronger effect of deterministic selection events in the plastisphere than in soil. We observed a severe disruption of cooccurrence network connectivity in plastisphere communities in contrast to bulk soil communities. This study closes the knowledge gap on plastic debris in Sub-Saharan terrestrial environments, and the observed effects on archaea and cooccurrence networks suggest negative impacts on nitrification and stability of microbial communities.

Glacier ice algae of the streptophyte genus Ancylonema bloom on glaciers globally, including the Greenland Ice Sheet. These algae survive under extreme high light conditions in the summer, as well as under very low light or total darkness during (polar) winters and winter burial under snow. However, little is known about the cellular mechanisms underpinning glacier ice algae ecophysiological plasticity in response to extreme light availability. To address this knowledge gap, we evaluated the response of Ancylonema-dominated taxa in samples from the Greenland Ice Sheet to light and dark conditions during a 12-day period using combined multi-omics analyses. The microbial community was not substantially altered during the 12 days of dark incubation, however transcriptomic analysis demonstrated that the algae-associated heterotrophs became more active in the dark. In contrast, we identified a striking algal transcriptome stability in light conditions, in addition to high oxidative stress responses and evidence for high photosystem protein turnover. We also identified transcriptional reprogramming linked to sugar uptake and phytohormone signalling during dark incubation. These results provide crucial clues into the ability of glacier ice algae to adapt and survive in a harsh and extremely variable light environment.

The relationship between, and joint selection on, a host and its microbes-the holobiont-can impact evolutionary and ecological outcomes of the host and its microbial community. We develop an agent-based modelling framework for understanding the ecological dynamics of hosts and their microbiomes. Our model incorporates numerous microbial generations per host generation allowing selection on both host and microbes. We then explore host and microbiome fitness and diversity in response to environmental change. We demonstrate that multiple microbial generations can buffer changes experienced across host lifetimes by smoothing environmental transitions. Our simulations reveal that microbial fitness and host fitness are at odds with each other when considering the impact of vertical inheritance of microbial communities from a host to its offspring-where high parent-offspring microbial transmission favours microbial fitness, while low transmission favours host fitness. These tradeoffs are minimized when microbial generation count per host generation is high. This may arise from 'cross-generational priority effects' which maintain diversity within the community and can subsequently enable selection of beneficial microbes by the host. Our model is extensible into new areas of holobiont research and provides novel insights into holobiont evolution under variable environmental conditions.

Constructed wetlands are widely used to reduce nutrient loading to downstream waters, but they can also emit methane, a potent greenhouse gas. This trade-off between water quality benefits and climate impacts is driven by microbial processes that remain poorly understood in winter. We examined microbial community composition and methane-cycling potential in surface water samples from constructed wetlands in two agricultural regions of Sweden during the winter season, focusing on the effects of emergent vegetation and environmental conditions. Western wetlands, characterized by higher total nitrogen and dissolved oxygen, exhibited significantly greater microbial diversity and more complex co-occurrence networks than eastern wetlands. At the phylum level, Actinobacteriota and Firmicutes were more abundant in the west, while Bacteroidota dominated the east. The effects of emergent vegetation were region-specific: in the west, vegetated zones supported higher diversity and enrichment of plant-associated taxa. Several taxa affiliated with methanotrophs showed higher relative abundance in vegetated zones of the western wetlands, suggesting vegetation may enhance methane oxidation potential in surface waters, even though methane concentrations were similar. Overall, winter microbial networks remained structured, emphasizing the need for integrated microbial and biogeochemical studies to guide wetland design features, such as vegetation and nutrient regimes, that support both methane mitigation and nutrient retention in cold-climate agricultural landscapes.

Commensal microbes play important roles in modulating host health through varied mechanisms. Enterococcus faecalis, a Gram-positive commensal bacterium found across a wide range of hosts, has the potential to benefit its host through probiotic, antimicrobial and detoxification properties. However, it can also cause adverse effects, disrupting the host's healthy microbial communities and responses to co-stressors. Its context-dependent impact on the health of the agriculturally important pollinator - Apis mellifera - has been sparsely explored. Here, we examined the effects on honey bee brood survivorship and development when exposed at different concentrations and when co-exposed with chemical stressors (acetamiprid, thymol, glyphosate, and a mixture of the three). We found high doses of E. faecalis significantly reduced larval survivorship and size of brood at multiple developmental stages. Conversely, we found that low doses of E. faecalis increased larval size when individuals were co-exposed to the pesticide mixture. We also found that glyphosate alone and the pesticide mixture reduced the mass of brown-eyed pupae. These results are the first to show the dual role of E. faecalis in honey bee health is dependent on the concentration of the microbe and the co-stressors that brood are exposed to.

Plastics in the world's oceans are exposed to diverse environmental stressors that accelerate fragmentation and the leaching of associated additives. The impact of potentially toxic plastic degradation products and additives on marine microorganisms remains poorly understood. We assessed the impact of plastic leachate on marine microbial communities in vitro by exposure to one of four plastic leachates [from linear low-density polyethylene (LLPDE), polyamide-6 (or polycaprolactam; PA6), polyethylene terephthalate (PET), and polylactic acid (PLA)], prepared by immersing plastics in artificial seawater salts broth for three months at 80°C. Microbial communities were then exposed to different leachates. PLA-leachate-exposed communities differed significantly in composition from other plastic-leachate-exposed communities (PERMANOVA, P=0.001) as assessed by 16S rRNA gene and ITS region amplicon sequencing. Communities exposed to PLA leachate contained a higher proportion of Proteobacteria, specifically Halomonas spp. Greater relative abundances of Psathyrellaceae fungi also distinguished PLA-leachate communities. Despite significant differences in the structure of communities exposed to PLA leachate, we found no difference in the relative abundances of differentially expressed gene transcripts associated with known plastic degradation genes. While biodegradable plastics persist for shorter times in the environment than traditional plastics, our study indicates the potential for these plastic types to impact marine microbial communities.