Microbial Ecology最新文献

Spontaneous afforestation following land abandonment has been increasingly recognized as a nature-based solution to mitigate climate change and provide measurable benefits to biodiversity. However, afforestation effects on biodiversity, particularly on soil microbial communities, are still poorly characterized, with most previous studies focusing on artificial plantations rather than forest rewilding dynamics. Here, we assessed changes in topsoil physical-chemical properties and related dynamics of bacterial and fungal community composition and structure following spontaneous afforestation of abandoned grasslands in Northeast Italy over the last 70 years. With a space-for-time approach, we selected four chronosequences representing different successional stages: grassland, early (2000-2020), intermediate (1978-2000), and late (1954-1978). Results showed that spontaneous afforestation progressively reduced topsoil pH and total phosphorus (P), while soil organic carbon (SOC), nitrogen (N), and C:N ratio increased. Correspondingly, the overall α-diversity of the fungal community, assessed by ITS DNA metabarcoding, progressively decreased after an initial increase from grassland conditions, following substrate acidification and trophic specialization. Bacterial diversity, assessed by 16S DNA metabarcoding, was highest at the initial stages, then progressively decreased at later stages, likely limited by lower organic matter quality. Shifts of fungal community composition included an increase of ectomycorrhizal Basidiomycota linked to topsoil's higher SOC, N, and C:N ratio. Differently, bacterial community composition responded substantially to pH, with topsoil acidity favoring Proteobacteria (Pseudomonadota) and Acidobacteria (Acidobacteriota) at the late afforestation stages. Our findings provide a first contribution to clarify how fungi and bacteria respond to spontaneous afforestation. This is particularly relevant in the context of climate change mitigation, considering the fundamental role of microorganisms in shaping soil carbon storage dynamics.

Exploring endospheric and rhizospheric microbiomes and their associations can help us to understand the pathological status of capsicum (Capsicum annuum L.) for implementing appropriate management strategies. To elucidate the differences among plants with distinct pathological status in the communities and functions of the endospheric and rhizospheric microbiomes, the samples of healthy and diseased capsicum plants, along with their rhizosphere soils, were collected from a long-term cultivation field. The results indicated a higher bacterial richness in the healthy rhizosphere than in the diseased rhizosphere (P < 0.05), with rhizospheric bacterial diversity surpassing endospheric bacterial diversity. The community assemblies of both the endospheric and rhizospheric microbiomes were driven by a combination of stochastic and deterministic processes, with the stochastic processes playing a primary role. The majority of co-enriched taxa in the healthy endophyte and rhizosphere mainly belonged to bacterial Proteobacteria, Actinobacteria, and Firmicutes, as well as fungal Ascomycota. Most of the bacterial indicators, primarily Alphaproteobacteria and Actinobacteria, were enriched in the healthy rhizosphere, but not in the diseased rhizosphere. In addition, most of the fungal indicators were enriched in both the healthy and diseased endosphere. The diseased endophyte constituted a less complex and stable microbial community than the healthy endophyte, and meanwhile, the diseased rhizosphere exhibited a higher complexity but lower stability than the healthy rhizosphere. Notably, only a microbial function, namely biosynthesis of other secondary metabolites, was higher in the healthy endophytes than in the diseased endophyte. These findings indicated the distinct responses of rhizospheric and endospheric microbiomes to capsicum pathological status, and in particular, provided a new insight into leveraging soil and plant microbial resources to enhance agriculture production.

Mezcal, a traditional Mexican alcoholic beverage, has been a vital source of livelihood for indigenous and rural communities for centuries. However, increasing international demand is exerting pressure on natural resources and encouraging intensive agricultural practices. This study investigates the impact of management practices (wild, traditional, and conventional) and environmental factors on the microbial communities associated with Agave angustifolia, a key species in mezcal production. High-throughput sequencing of the 16S rRNA and ITS2 gene regions revealed distinct prokaryotic and fungal community structures across different plant compartments (endosphere, episphere, and soil), identifying 8214 prokaryotic and 7459 fungal ASVs. Core microbial communities were dominated by Proteobacteria, Actinobacteria, Ascomycota, and Basidiomycota. Alpha diversity analyses showed significant increases in prokaryotic diversity from the endosphere to soil, while fungal diversity remained stable. Notably, conventional management practices were associated with reductions in beneficial microbial taxa. Environmental factors such as precipitation and temperature significantly influenced microbial diversity and composition, especially in the rhizosphere. Beta diversity patterns underscored the strong impact of plant compartment, with management practices and aridity further shaping microbial communities. These results reveal the intricate interactions between management practices, environmental conditions, and microbial diversity, providing valuable insights for the sustainable cultivation of A. angustifolia.

In the past decades, dozens of invasion hypotheses have been proposed to elucidate the invasion mechanisms of exotic species. Among them, the accumulation of local pathogens hypothesis (ALPH) posits that invasive plants can accumulate local generalist pathogens that have more negative effect on native species than on themselves; as a result, invasive plants might gain competitive advantages that eventually lead to their invasion success. However, research on this topic is still quite insufficient. In this context, we performed a comprehensive literature survey in order to provide a detailed description of the origin and theoretical framework of ALPH; in addition, challenges in contemporary research such as limitations in technical methods and the complexity of interactions between plants and soil microorganisms, as well as future directions of ALPH research, are also discussed in this review. So far, there are less than ten case studies supporting ALPH; therefore, more work is needed to demonstrate whether ALPH is a suitable hypothesis to elucidate the invasion success of certain plant species.

The marine microbiome arouses an increasing interest, aimed at better understanding coral reef biodiversity, coral resilience, and identifying bioindicators of ecosystem health. The present study is a microbiome mining of three environmentally contrasted sites along the Hermitage fringing reef of La Réunion Island (Western Indian Ocean). This mining aims to identify bioindicators of reef health to assist managers in preserving the fringing reefs of La Réunion. The watersheds of the fringing reefs are small, steeply sloped, and are impacted by human activities with significant land use changes and hydrological modifications along the coast and up to mid-altitudes. Sediment, seawater, and coral rubble were sampled in austral summer and winter at each site. For each compartment, bacterial, fungal, microalgal, and protist communities were characterized by high throughput DNA sequencing methodology. Results show that the reef microbiome composition varied greatly with seasons and reef compartments, but variations were different among targeted markers. No significant variation among sites was observed. Relevant bioindicators were highlighted per taxonomic groups such as the Firmicutes:Bacteroidota ratio (8.4%:7.0%), the genera Vibrio (25.2%) and Photobacterium (12.5%) dominating bacteria; the Ascomycota:Basidiomycota ratio (63.1%:36.1%), the genera Aspergillus (40.9%) and Cladosporium (16.2%) dominating fungi; the genus Ostreobium (81.5%) in Chlorophyta taxon for microalgae; and the groups of Dinoflagellata (63.3%) and Diatomea (22.6%) within the protista comprising two dominant genera: Symbiodinium (41.7%) and Pelagodinium (27.8%). This study highlights that the identified bioindicators, mainly in seawater and sediment reef compartments, could be targeted by reef conservation stakeholders to better monitor La Réunion Island's reef state of health and to improve management plans.

The ecological niche separation of microbial interactions in forest ecosystems is critical to maintaining ecological balance and biodiversity and has yet to be comprehensively explored in microbial ecology. This study investigated the impacts of soil properties on microbial interactions and carbon metabolism potential in forest soils across 67 sites in China. Using redundancy analysis and random forest models, we identified soil pH and dissolved organic matter (DOM) aromaticity as the primary drivers of microbial interactions, representing abiotic conditions and resource niches, respectively. Our network comparison results highlighted significant differences in microbial interactions between acidic and non-acidic soils, suggesting the critical influences of abiotic conditions on microbial interactions. Conversely, abiotic resource niches played a more pivotal role in shaping the carbon metabolism of soil microbes, supporting the concept that resource niche-based processes drive microbial carbon cycling. Additionally, we demonstrated that microbial interactions contributed significantly to ecosystem function stability and served as potential ecological indicators of microbial functional resilience under environmental stress. These insights emphasize the critical need to preserve microbial interactions for effective forest ecosystem management and projection of ecological outcomes in response to future environmental changes.

With amphibians still holding the record as the most threatened class of terrestrial vertebrates, their skin microbiota has been shown to play a relevant role in their survival in a fast-changing world. Yet little is known about how abiotic factors associated with different aquatic habitats impact these skin microorganisms. Here we chose the yellow-bellied toad (Bombina variegata), a small anuran that colonizes a wide range of wetland habitats, to investigate how the diversity and composition of both its bacterial and fungal skin communities vary across different habitats and with water characteristics (temperature, pH, and dissolved oxygen) of these habitats. Skin microbiota was sampled from 14 sites in the Province of Trento (Italy), including natural pools, ephemeral ponds, irrigation tanks, and farm ponds. Interestingly, the diversity of the two microbial components was also highly correlated. Close associations between both the diversity and composition of water and skin communities were noted for each habitat and sampling site, suggesting that water bodies actively contribute to the skin microbiota assemblage. In addition, water pH, temperature, and dissolved oxygen affected both bacterial and fungal diversity of skin. We confirmed the presence of Batrachochytrium dendrobatidis in skin samples of animals collected from eight waterbodies, as well as more than 60 microbial taxa previously associated with resistance to this pathogen. We concluded that both skin bacterial and fungal communities appear to be influenced by each other as well as by environmental communities and conditions, and these relationships connecting the whole ecosystem should be considered in future research concerning amphibian conservation.

Cheese production involves various lactic acid bacteria (LAB) that break down lactose, milk proteins, and fats, producing key nutrients and influencing the cheese's flavor. They form communities that play a crucial role in determining the cheese's organoleptic properties. The composition of cheeses' microbial communities is shaped by physicochemical factors (e.g., temperature, pH, and salinity) and biological factors (i.e. microbial interactions). While starter cultures are introduced to control these communities, non-starter LAB represent a significant portion of the final microbial assemblage, but their interactions remain unclear. LAB often produce bacteriocins, antimicrobial peptides that antagonize other bacteria, but their role within LAB communities is not fully understood. This study aimed to assess the impact of bacteriocin production on LAB diversity in cheese, using Enterococcus as a model organism, a common bacteriocin producer. We analyzed enterocin production of enterococcal isolates by antimicrobial assays and microbial diversity differences in raw milk cheeses by two approaches: 16S RNA gene amplicon metagenomic sequencing for the whole microbial community and multi-locus sequence analysis (MLSA) for the enterococcal diversity. Our results revealed that LAB communities were dominated by lactococci, lactobacilli, and streptococci, with enterococci present in lower numbers. However, cheeses containing bacteriocin-producing enterococci exhibited higher microbial diversity. Interestingly, the highest diversity occurred at low levels of bacteriocin producers, but this effect was not observed within enterococcal populations. These findings suggest that bacteriocin production plays a key role in shaping LAB communities during cheese ripening, although further research is needed to understand its broader implications in other microbial ecosystems.

Microbial biotechnology employs techniques that rely on the natural interactions that occur in ecosystems. Bacteria, including rhizobacteria, play an important role in plant growth, providing crops with an alternative that can mitigate the negative effects of abiotic stress, such as those caused by saline environments, and increase the excessive use of chemical fertilizers. The present study examined the promoting potential of bacterial isolates obtained from the rhizospheric soil and roots of the Asparagus officinalis cultivar UF-157 F2 in Viru, la Libertad, Peru. This region has high soil salinity levels. Seventeen strains were isolated, four of which are major potential plant growth-promoting traits, and were characterized based on their morphological and molecular characteristics. These salt-tolerant bacteria were screened for phosphate solubilization, indole acetic acid, deaminase activity, and molecular characterization by 16S rDNA sequencing. Fifteen samples were from saline soils of A. officinalis plants in the northern coastal desert of San Jose, Lambayeque, Peru. The bacterial isolates were screened in a range of salt tolerances from 3 to 6%. Isolates 05, 08, 09, and 11 presented maximum salt tolerance, ammonium quantification, phosphate solubilization, and IAA production. The four isolates were identified by sequencing the amplified 16S rRNA gene and were found to be Enterobacter sp. 05 (OQ885483), Enterobacter sp. 08 (OQ885484), Pseudomonas sp. 09 (OR398704) and Klebsiella sp. 11 (OR398705). These microorganisms promoted the germination of Zea mays L. plants, increased the germination rates in the treatments with chemical fertilizers at 100% and 50%, and the PGPRs increased the height and length of the roots 40 days after planting. The beneficial effects of salt-tolerant PGPR isolates isolated from saline environments may lead to new species that can be used to overcome the detrimental effects of salt stress on plants. The biochemical response and inoculation of the three isolates prove the potential of these strains as sources of products to develop new compounds, confirming their potential as biofertilizers for saline environments.