Microbial Ecology最新文献

Fungal endophytes play an important role in improving the health and productivity of native and cultivated plant species. Despite their ecological and industrial importance, few eucalypt species have been studied in terms of their endophyte communities. We examined the seasonal and spatial dynamics of fungal leaf endophytes in the model species, Eucalyptus crebra (narrow-leaved ironbark), using ITS-based amplicon sequencing. Alpha and beta diversity analyses revealed significantly higher species richness in summer compared to autumn and spring. Similarly, two-way ANOVA analysis showed significantly higher species diversity in summer compared to autumn (observed p < 0.001, Chao1 p < 0.005) and spring (observed p < 0.005, Chao1 p < 0.005). No difference in Shannon index was observed among different canopy levels across the season. Beta-diversity showed differences in fungal composition across the seasons and at various canopy levels based on unweighted UniFrac distance metric (PERMANOVA season p < 0.001, canopy p < 0.05), signifying distinct separation of fungi based on presence-absence. Ascomycota was the most abundant and diverse phylum and was present throughout the year. In contrast, Basidiomycota was only observed during cooler and drier seasons. Neofusicoccum was the most abundant genus, but distribution fluctuated significantly across the seasons. Pestalotiopsis and Neopestalotiopsis were most abundant in the low leaf canopy, whereas Pseudosydowia was most abundant in the high canopy. This study indicates that the diversity and abundance of endophytic fungi in the leaves of healthy E. crebra trees fluctuate seasonally and across canopy levels. The data generated can be used as a baseline for assessing and potentially modulating the health of E. crebra and other important Eucalyptus spp.

The gut microbiota of vertebrates is malleable and may be shaped by both intrinsic and extrinsic factors. Here, the effect that geography has on the cloacal microbiota of two species of Australian freshwater chelonians, eastern longneck turtle (Chelodina longicollis) and Macquarie River turtle (Emydura macquarii), captured from waterbodies with different levels of anthropogenic pressure was investigated. We analysed the microbiota composition, structure and diversity through 16S rRNA gene amplicon sequencing. It was hypothesised that animals from less disturbed environments would harbour a more diverse cloacal microbial population. The cloacal microbiotas from 93 turtles (C. longicollis n = 78; E. macquarii n = 15), from five locations, were analysed. For both species, the most predominant phylum was Proteobacteria. Cloacal microbiota alpha diversity varied significantly between the C. longicollis from all locations, but no differences were found for E. macquarii. In C. longicollis, turtles from wetlands within the centre of Melbourne had the lowest alpha diversity metrics, while the highest alpha diversity values were seen in turtles captured from an undisturbed rural waterbody. Beta diversity, obtained by weighted UniFrac distance, showed significant differences between locations of capture for both species of turtles in this investigation. For C. longicollis, 87 biomarkers were identified responsible for explaining differences between locations, and in E. macquarii, 42 biomarkers were found. This is the first study to explore the cloacal microbiota composition of the eastern longneck turtle and gives greater insight into microbial community structures in Macquarie River turtles. Our study demonstrated that cloacal microbiota composition of freshwater turtles was significantly influenced by locality and that disrupted environments may reduce microbial diversity in C. longicollis. Interestingly, we discovered that the effects of location contrasted significantly between species for alpha diversity with differences discovered for C. longicollis but not E. macquarii. However, for both species, beta diversity was notably influenced by habitat type. These results highlight the need to interpret chelonian microbiota data in the context of geography and human disturbance of the environment.

The single-step methioninase-mediated degradation of methionine (as a sulfur containing amino acid) is a reaction at the interface of carbon, nitrogen, sulfur, and methane metabolism in microbes. This enzyme also has therapeutic application due to its role in starving auxotrophic cancer cells. Applying our refined in silico screening pipeline on 33,469 publicly available genome assemblies and 1878 metagenome assembled genomes/single-cell amplified genomes from brackish waters of the Caspian Sea and the Fennoscandian Shield deep groundwater resulted in recovering 1845 methioninases. The majority of recovered methioninases belong to representatives of phyla Proteobacteria (50%), Firmicutes (29%), and Firmicutes_A (13%). Prevalence of methioninase among anaerobic microbes and in the anoxic deep groundwater together with the relevance of its products for energy conservation in anaerobic metabolism highlights such environments as desirable targets for screening novel methioninases and resolving its contribution to microbial metabolism and interactions. Among archaea, majority of detected methioninases are from representatives of Methanosarcina that are able to use methanethiol, the sulfur containing product from methionine degradation, as a precursor for methanogenesis. Branching just outside these archaeal methioninases in the phylogenetic tree, we recovered three methioninases belonging to representatives of Patescibacteria reconstructed from deep groundwater metagenomes. We hypothesize that methioninase in Patescibacteria could contribute to their syntrophic interactions where their methanogenic partners/hosts benefit from the produced 2-oxobutyrate and methanethiol. Our results underscore the significance of accounting for specific ecological niche in screening for enzyme variates with desired characteristics. Finally, complementing of our findings with experimental validation of methioninase activity confirms the potential of our in silico screening in clarifying the peculiar ecological role of methioninase in anoxic environments.

Temporal variation during the assembly of arbuscular mycorrhizal (AM) fungal communities within plant roots have been posited as critical drivers of the plant-fungal symbiotic outcomes. However, functional implications of these dynamics for the host plant remain poorly understood. We conducted a controlled pot experiment with Sorghum bicolor to investigate how temporal shifts in AM fungal community composition and phylogenetic diversity influence plant growth and phosphorus responses to the symbiosis. We characterised the root-colonising AM fungal communities across three time points and explored their community assembly processes by analysing their phylogenetic diversity and employing joint species distribution modelling with the Hierarchical Modelling of Species Communities (HMSC) framework. We found strong AM fungal turnover through time with a high phylogenetic signal, indicating recruitment of phylogenetically clustered AM fungal species in the host. This temporal phylogenetic clustering of communities coincided with marked increases in plant biomass and phosphorus responses to the AM fungal symbiosis, suggesting that host selection for specific fungi may be a key determinant of these benefits.

Nitrogen is often a limiting nutrient for microbial communities and plants in glacier forefields. Nitrogen-fixing microorganisms (diazotrophs) play an important role in providing bioavailable nitrogen, with their composition determining the nitrogen-fixating capacities. This study investigates the spatial and temporal dynamics of diazotrophs in the forefields of three Tibetan glaciers: Qiangyong, Kuoqionggangri, and Longxiazailongba. We collected soil samples from recently deglaciated barren grounds, and also along an ecosystem succession transect at Kuoqionggangri glacier, encompassing barren ground, herb steppe, legume steppe, and alpine meadow ecosystems. Our finding revealed abundant and diverse diazotrophs in the recently deglaciated barren ground. They are taxonomically affiliated with anaerobic Bradyrhizobium, Desulfobulbus, and Pelobacter, which may be relics from subglacial sediments. The vegetated soils (herb steppe, legume steppe, and alpine meadow) were dominated by phototrophic Nostoc and Anabaena, as well as symbiotic Sinorhizobium. Soil physicochemical parameters, such as soil organic carbon, pH, and nitrate ion, significantly influenced diazotroph community structure. This study highlights the critical role of diazotrophs in mitigating nitrogen limitation during early ecosystem development in glacier forefields. Understanding the distribution and ecological drivers of diazotrophs in these rapidly changing environments provides insights into biogeochemical cycling and ecosystem resilience under climate change.

Saline shallow lakes in arid and semi-arid regions frequently undergo drying episodes, leading to significant variations in salinity and water availability. Research on the impacts of salinity and drought on the structure and function of biofilms in hypersaline shallow lakes is limited. This study aimed to understand the potential changes of biofilms in playa-lake sediments during the drying process. Sediments were sampled at different depths (surface, subsurface) and hydrological periods (wet, retraction, and dry), which included a decrease in water activity (a_w, the availability of water for microbial use) from 0.99 to 0.72. a_w reduction caused a greater effect on functional variables compared to structural variables, indicating the high resistance of the studied biofilms to changes in salinity and water availability. Respiration and hydrolytic extracellular enzyme activities exhibited higher values under high a_w, while phenol oxidase activity and prokaryote biomass increased at lower a_w. This shift occurred at both depths but was more pronounced at the surface, possibly due to the more extreme conditions (up to 0.7 a_w). The increased levels of extracellular polymeric substances and carotenoids developed at low a_w may help protect microorganisms in high salinity and drought environments. However, these harsh conditions may interfere with the activity of hydrolytic enzymes and their producers, while promoting the growth of resistant prokaryotes and their capacity to obtain C and N sources from recalcitrant compounds. The resilience of biofilms in hypersaline lakes under extreme conditions is given by their resistant biochemichal structure and the adaptability of their microbial functioning.

Arbuscular mycorrhizal fungi (AMF) live in a community in the roots of host plants. Still, the patterns and factors that drive their spatiality and cohabitation remain uncovered, particularly that of trees in planted forests, which we aimed to clarify in Cryptomeria japonica, a major plantation tree in Japan. We analyzed 65 paired root and soil samples of Cryptomeria japonica trees collected from 11 microsite (MS) plots at two environmentally different forest sites in central Japan and measured soil pH, total phosphorus (TP), C, N, and the carbon-to-nitrogen ratio. Root AMF communities were recovered using Illumina's next-generation amplicon sequencing targeting the small subunit of ribosomal DNA. We detected more than 500 AMF OTUs at each site but only three belonging to Dominikia, Rhizophagus, and Sclerocystis were dominant in the roots of C. japonica, detected each at an average relative abundance higher than 20%. Two showed negatively correlated spatial distributions and different associations with soil pH. Similarly, the physicochemical properties at MSs significantly determined the AMF assemblages in the roots of C. japonica. Dominikia, Rhizophagus, and Sclerocystis coexist in the roots of C. japonica where soil physicochemical properties, particularly pH, determine their spatial dynamic, turnovers, and cohabitation patterns. These findings highlight the importance of simultaneous colonization of plants by multiple AMF.

Saline lakes, characterized by high salinity and limited nutrient availability, provide an ideal environment for studying extreme halophiles and their biogeochemical processes. The present study examined prokaryotic microbial communities and their ecological functions in lentic sediments (with the salinity gradient and time series) using 16S rRNA amplicon sequencing and a metagenomic approach. Our findings revealed a negative correlation between microbial diversity and salinity. The notable predominance of Archaea in high-salinity lakes signified a considerable alteration in the composition of the microbial community. The results indicate that elevated salinity promotes homogeneous selection pressures, causing substantial alterations in microbial diversity and community structure, and simultaneously hindering interactions among microorganisms. This results in a notable decrease in the complexity of microbial ecological networks, ultimately influencing the overall ecological functional responses of microbial communities such as carbon fixation, sulfur, and nitrogen metabolism. Overall, our findings reveal salinity drives a notable predominance of Archaea, selects for species adapted to extreme conditions, and decreases microbial community complexity within saline lake ecosystems.

Control of fungal phytopathogens is a significant challenge in modern agriculture. The widespread use of chemical fungicides to control these pathogens often leads to environmental and food contamination. An eco-friendly alternative that can help reduce reliance on these chemicals is plant growth-promoting bacteria (PGPB), particularly those of the genus Paenibacillus, which appear to be highly effective. The review aims to summarize the existing knowledge on the potential of Paenibacillus spp. as fungal biocontrol agents, identify knowledge gaps, and answer whether other species of the genus Paenibacillus, in addition to Paenibacillus polymyxa, can also be effective biocontrol agents. Paenibacillus spp. can combat plant phytopathogens through various mechanisms, including the production of lipopeptides (such as fusaricidin, paenimyxin, and pelgipeptin), the induction of systemic resistance (ISR), hydrolytic enzymes (chitinase, cellulase, and glucanase), and volatile organic compounds. These properties enable Paenibacillus strains to suppress the growth of fungi such as Fusarium oxysporum, F. solani, Rhizoctonia solani, Botrytis cinerea, or Colletotrichum gloeosporioides. Notably, several strains of Paenibacillus, including P. polymyxa, P. illinoisensis KJA-424, P. lentimorbus B-30488, and P. elgii JCK1400, have demonstrated efficacy in controlling fungal diseases in plants. Importantly, many formulations with Paenibacillus strains have already been patented, and some are commercially available, but most of them contain only P. polymyxa. Nevertheless, considering the data presented in this review, we believe that other strains from the Paenibacillus genus (besides P. polymyxa) will also be commercialized and used in plant protection in the future. Importantly, there is still limited information regarding their impact on the native microbiota, particularly from the metataxonomic and metagenomic perspectives. Expanding knowledge in this area could enhance the effectiveness of biocontrol agents containing Paenibacillus spp., ensuring safe and sustainable use of biological fungicides.

Heavy metal (HM) contaminants are the emerging driving force for reshaping the microflora of plants by eradicating the non-tolerance and non-resistant microbes via their lethal effects. Seeds served as a prime source of ancestral microbial diversity hereditary transfer from generation to generation. However, the problem arises when they got exposed to metal contamination, does metal pollutant disrupt the delicate balance of microbial communities within seeds and lead to shifts in their microflora across generations. In this study, the endophytic community within Zea mays seeds was compared across three distinct regions in Yunnan province, China: a HM-contaminated site Ayika (AK), less-contaminated site Sanduoduo (SD), and a non-contaminated Site Dali (DL). High-throughput sequencing techniques were employed to analyze the microbial communities. A total of 492,177 high-quality reads for bacterial communities and 1,001,229 optimized sequences for fungal communities were obtained. These sequences were assigned to 502 and 239 operational taxonomic units (OTUs) for bacteria and fungi, respectively. A higher diversity was recorded in AK samples than in SD and DL. Microbial community structure analysis showed higher diversity and significant fluctuation in specific taxa abundance in the metal-polluted samples exhibiting higher response of microbial flora to HM. In AK samples, bacterial genera such as Gordonia and Burkholderia-Caballeronia-Paraburkholderia were dominant, while in SD Pseudomonas and Streptomyces were dominant. Among the fungal taxa, Fusarium, Saccharomycopsis, and Lecanicillium were prevalent in HM-contaminated sites. Our finding revealed the influential effect of HM contaminants on reshaping the seed microbiome of the Zea mays, showing both the resilience of certain important microbial taxa as well the shifts in the diversity in the contaminated and pristine conditions. The knowledge will benefit to develop effective soil remediation, reclamation, and crop management techniques, and eventually assisting in the extenuation of metal pollution's adverse effects on plant health and agricultural productivity.