分子生态网络揭示冶金微生物对能源底物的响应

通过分析不同铁硫比的能源底物驯化下冶金微生物群落的演替过程,基于分子生态网络揭示冶金微生物对能源底物的响应特征。对富铁少硫、富硫少铁条件下不同驯化批次的微生物样本进行高通量测序,分析物种组成,比较冶金微生物群落的α多样性和β多样性,并构建分子生态网络,探究驯化过程微生物之间的相互作用关系。鉴定关键物种,分析冶金微生物群落对能源底物的响应。研究发现在基于不同能源底物驯化过程中,富铁少硫群落的优势物种为嗜酸氧化亚铁硫杆菌Acidithiobacillus ferrooxidans和铁氧化嗜酸硫杆菌A. ferriphilus;而富硫少铁群落经过3个批次的驯化,氧化硫硫杆菌A. thiooxidans占比高达90%。α、β多样性分析结果表明,富硫少铁能源底物驯化过程使冶金微生物群落多样性降低,且随着驯化批次的增加群落组成发生显著变化。分子生态网络分析显示关键物种均为低丰度稀有物种,富硫少铁条件下菌种间具有更紧密的互作共生关系,群落更加稳定。通过该驯化实验,明确了不同能源底物对冶金微生物群落的影响。采用富硫少铁能源底物驯化冶金微生物,使冶金微生物群落更加稳定,有助于优势物种高效发挥铁、硫氧化功能,促进硫化矿物的氧化溶解,为生物冶金工业育种微生物群落的定向驯化提供理论基础。     

Unusual fungal niches

Fungi are found in all aerobic ecosystems, colonizing a diversity of substrates and performing a wide diversity of functions, some of which are not well understood. Many spices of fungi are cosmopolitan and generalists or habitats. Unusual fungal niches are habitats where extreme conditions would be expected to prevent the development of a mycobiota. In this review we describe five unusual fungal habitats in which fungi occupy poorly understood niches: Antarctic dry valleys, high Arctic glaciers, salt flats and salterns, hypersaline microbial mats and plant trichomes. Yeasts, black yeast-like fungi, melanized filamentous species as well as representatives of Aspergillus and Penicillium seem to be dominant among the mycobiota adapted to cold and saline niches. Plant trichomes appear to be a taxa. The advent of new sequencing technologies is helping to elucidate the microbial diversity in many ecosystems, but more studies are needed to document the functional role of fungi in the microbial communities thriving in these unusual environments.     

Dealing with water stress and microbial preservation

The relevance of preserving microorganisms has been well accepted for several decades. Interest is now shifting towards investigating adequate preservation methods to improve microbial survival rates and to preserve new taxa of previously considered unculturable microorganisms. In addition, a growing interest in preserving fragile microbial consortia or communities with biotechnological interest motivates the improvement of preservation methods. In the present study, we reviewed the effect of water availability in microbial diversity shift. We describe the effect of drought on microorganisms at the molecular level and their molecular responses to this life-threatening challenge focusing on the production of xeroprotectants. We also review the interspecies interactions of those drought-tolerant microorganisms with other sensitive organisms including neighbouring prokaryotes and eukaryotes such as plants, and the potential role of these microorganisms at determining the ecological composition of stressed environments. We emphasize the importance of applying the knowledge derived from the molecular mechanisms used by desiccation-tolerant microorganisms for the improvement of the preservation techniques. An overview of the current and newer techniques for preserving microorganisms and microbial communities is provided. The biotechnological interest in preserving pure cultures, microbial consortia and communities is also discussed.     

The characterisation of eukaryotic microbial communities on sandstone buildings in Belfast,UK, using TRFLP and 454 pyrosequencing

Eukaryotic microorganisms, notably microbial algae and fungi, can have a major impact on the biodeterioration of building stone, particularly when they form green biofilms. However, comparatively little is known about the composition and structure of eukaryotic communities living on the surface of stone. The twin aims of this study were to a) characterise algal and fungal communities living on heritage structures in Belfast, UK and b) to investigate the relationship between eukaryotic community composition and a variety of substrate characteristics. We used molecular techniques (TRFLP and 454 pyrosequencing) to characterise the communities. We found unexpectedly high levels of taxonomic richness in algal communities, but low overall levels of diversity in both the algal and the fungal assemblages resulting from inequitable distributions of taxa. Our findings suggest the existence of a small pool of cosmopolitan algal species and relatively homogeneous algal communities on sandstone structures. In contrast, fungal communities were much richer and more spatially heterogeneous. It is likely that the aggressive chemical cleaning of one of the structures in the 1980s has had an ongoing impact on microbial community structure. Furthermore, whilst substrate characteristics seem to impact on the abundance/biomass of eukaryotic microbial communities, they do not influence diversity.     

Drosophila regulate yeast density and increase yeast community similarity in a natural substrate

Drosophila melanogaster adults and larvae, but especially larvae, had profound effects on the densities and community structure of yeasts that developed in banana fruits. Pieces of fruit exposed to adult female flies previously fed fly-conditioned bananas developed higher yeast densities than pieces of the same fruits that were not exposed to flies, supporting previous suggestions that adult Drosophila vector yeasts to new substrates. However, larvae alone had dramatic effects on yeast density and species composition. When yeast densities were compared in pieces of the same fruits assigned to different treatments, fruits that developed low yeast densities in the absence of flies developed significantly higher yeast densities when exposed to larvae. Across all of the fruits, larvae regulated yeast densities within narrow limits, as compared to a much wider range of yeast densities that developed in pieces of the same fruits not exposed to flies. Larvae also affected yeast species composition, dramatically reducing species diversity across fruits, reducing variation in yeast communities from one fruit to the next (beta diversity), and encouraging the consistent development of a yeast community composed of three species of yeast (Candida californica, C. zemplinina, and Pichia kluvyeri), all of which were palatable to larvae. Larvae excreted viable cells of these three yeast species in their fecal pools, and discouraged the growth of filamentous fungi, processes which may have contributed to their effects on the yeast communities in banana fruits. These and other findings suggest that D. melanogaster adults and their larval offspring together engage in 'niche construction', facilitating a predictable microbial environment in the fruit substrates in which the larvae live and develop.     

Fungal diversity increases soil fungistasis and resistance to microbial invasion by a non resident species

Biodiversity decline is a major concern for ecosystem functioning. Recent research efforts have been mostly focused on terrestrial plants, while, despite their importance in both natural and artificial ecosystems, little is known about soil microbial communities. This work aims at investigating the effects of fungal species richness on soil invasion by non resident microbes. Synthetic fungal communities with a species diversity ranging from 1 to 8 were assembled in laboratory microcosms and used in three factorial experiments to assess the effect of diversity on soil fungistasis, microbial invasion of soil amended with plant litter and of plant rhizosphere. The capability of different microbes to colonize environments characterized by different resident microbial communities was measured. The number of microbial species in the microcosms positively affected soil fungistasis that was also induced more rapidly in presence of synthetic communities with more species. Moreover, the increase of resident fungal diversity dramatically reduced the invasibility of both soil and plant rhizosphere. We found lower variability of soil fungistasis and invasibility in microcosms with higher species richness of microbial communities. Our study pointed out the existence of negative relationships between fungal diversity and soil invasibility by non resident microbes. Therefore, the loss of microbial species may adversely affect ecosystem functionality under specific environmental conditions.     

TRFLP analysis reveals that fungi rather than bacteria are associated with premature yeast flocculation in brewing

Premature yeast flocculation (PYF) is a sporadic fermentation problem in the brewing industry that results in incomplete yeast utilization of fermentable sugars in wort. Culture-independent, PCR-based fingerprinting techniques were applied in this study to identify the associations between the occurrence of the PYF problem during brewery fermentation with barley malt-associated microbial communities (both bacteria and fungi). Striking differences in the microbial DNA fingerprint patterns for fungi between PYF positive (PYF +ve) and negative (PYF ?ve) barley malts were observed using the terminal restriction fragment length polymorphism (TRFLP) technique. The presence of terminal restriction fragments (TRFs) of 360–460 bp size range, for fungal HaeIII restriction enzyme-derived TRFLP profiles appeared to vary substantially between PYF +ve and PYF ?ve samples. The source of the barley malt did not influence the fungal taxa implicated in PYF. TRFLP analysis indicates bacterial taxa are unlikely to be important in causing PYF. Virtual digestion of fungal sequences tentatively linked HaeIII TRFs in the 360–460 bp size range to a diverse range of yeast/yeast-like species. Findings from this study suggest that direct monitoring of barley malt samples using molecular methods could potentially be an efficient and viable alternative for monitoring PYF during brewery fermentations.     

Spatial structure of epiphytic yeast communities on fruits of <Emphasis Type="Italic">Sorbus aucuparia</Emphasis> L.

The subject of this research is epiphytic yeast communities formed on the surface of Sorbus aucuparia. The object is to make quantitative assessment of the yeast communities’ differentiation of the same but distant substratum. Results of the nested ANOVA demonstrated that with increase in distances, there are increases in the variation of total number and relative abundance of the dominant yeast communities. The average similarity between groups of single fruits (Sørensen’s f Similarity Coefficient) regularly decreased with distance. The results demonstrate that the number and structure of separate yeast groups depend not only on ecological factors but also on proximity to other communities. Such aggregation in the distribution of the microorganisms’ species caused by migration and colonial resettlement should be taken into account when analyzing their diversity in natural habitats.     

Skin fungal assemblages of bats vary based on susceptibility to white-nose syndrome

Microbial skin assemblages, including fungal communities, can influence host resistance to infectious diseases. The diversity-invasibility hypothesis predicts that high-diversity communities are less easily invaded than species-poor communities, and thus diverse microbial communities may prevent pathogens from colonizing a host. To explore the hypothesis that host fungal communities mediate resistance to infection by fungal pathogens, we investigated characteristics of bat skin fungal communities as they relate to susceptibility to the emerging disease white-nose syndrome (WNS). Using a culture-based approach, we compared skin fungal assemblage characteristics of 10 bat species that differ in susceptibility to WNS across 10 eastern U.S. states. The fungal assemblages on WNS-susceptible bat species had significantly lower alpha diversity and abundance compared to WNS-resistant species. Overall fungal assemblage structure did not vary based on WNS-susceptibility, but several yeast species were differentially abundant on WNS-resistant bat species. One yeast species inhibited Pseudogymnoascus destructans (Pd), the causative agent on WNS, in vitro under certain conditions, suggesting a possible role in host protection. Further exploration of interactions between Pd and constituents of skin fungal assemblages may prove useful for predicting susceptibility of bat populations to WNS and for developing effective mitigation strategies.Subject terms: Microbiome, Fungal ecology     

Preliminary notes on yeasts associated with necrotic cactus stems from different localities in Brazil.

The yeast species found in necrotic stems of three columnar cacti (Pilosocereus machrisii, Pilosocereus vilaboensis, and Praecereus euchlorus) at eight localities in Brazil were described and a similarity analysis using Sorensen distances was used to compare the composition of yeast species at these localities. Of 56 necrotic cactus stems sampled, 32 produced yeast colonies. Ten species of yeast or yeast-like microorganisms were identified from 53 isolates, with Pichia cactophila, Candida sonorensis, Geotrichum sp., and Sporopachydermia cereana being the most common. The remaining species occurred in low proportions in the cacti surveyed. The similarity analysis provided a dendogram (UPGMA) that clustered the yeast communities from different cactus species and indicated that host cactus species was unimportant in this clustering.     

Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau

Permafrost represents an important understudied genetic resource. Soil microorganisms play important roles in regulating biogeochemical cycles and maintaining ecosystem function. However, our knowledge of patterns and drivers of permafrost microbial communities is limited over broad geographic scales. Using high‐throughput Illumina sequencing, this study compared soil bacterial, archaeal and fungal communities between the active and permafrost layers on the Tibetan Plateau. Our results indicated that microbial alpha diversity was significantly higher in the active layer than in the permafrost layer with the exception of fungal Shannon–Wiener index and Simpson's diversity index, and microbial community structures were significantly different between the two layers. Our results also revealed that environmental factors such as soil fertility (soil organic carbon, dissolved organic carbon and total nitrogen contents) were the primary drivers of the beta diversity of bacterial, archaeal and fungal communities in the active layer. In contrast, environmental variables such as the mean annual precipitation and total phosphorus played dominant roles in driving the microbial beta diversity in the permafrost layer. Spatial distance was important for predicting the bacterial and archaeal beta diversity in both the active and permafrost layers, but not for fungal communities. Collectively, these results demonstrated different driving factors of microbial beta diversity between the active layer and permafrost layer, implying that the drivers of the microbial beta diversity observed in the active layer cannot be used to predict the biogeographic patterns of the microbial beta diversity in the permafrost layer.     

The Vineyard Yeast Microbiome,a Mixed Model Microbial Map

Vineyards harbour a wide variety of microorganisms that play a pivotal role in pre- and post-harvest grape quality and will contribute significantly to the final aromatic properties of wine. The aim of the current study was to investigate the spatial distribution of microbial communities within and between individual vineyard management units. For the first time in such a study, we applied the Theory of Sampling (TOS) to sample gapes from adjacent and well established commercial vineyards within the same terroir unit and from several sampling points within each individual vineyard. Cultivation-based and molecular data sets were generated to capture the spatial heterogeneity in microbial populations within and between vineyards and analysed with novel mixed-model networks, which combine sample correlations and microbial community distribution probabilities. The data demonstrate that farming systems have a significant impact on fungal diversity but more importantly that there is significant species heterogeneity between samples in the same vineyard. Cultivation-based methods confirmed that while the same oxidative yeast species dominated in all vineyards, the least treated vineyard displayed significantly higher species richness, including many yeasts with biocontrol potential. The cultivatable yeast population was not fully representative of the more complex populations seen with molecular methods, and only the molecular data allowed discrimination amongst farming practices with multivariate and network analysis methods. Importantly, yeast species distribution is subject to significant intra-vineyard spatial fluctuations and the frequently reported heterogeneity of tank samples of grapes harvested from single vineyards at the same stage of ripeness might therefore, at least in part, be due to the differing microbiota in different sections of the vineyard.     

Dynamics of bacterial and fungal communities associated with eggshells during incubation

Microorganisms are closely associated with eggs and may play a determinant role in embryo survival. Yet, the majority of studies focusing on this association relied on culture‐based methodology, eventually leading to a skewed assessment of microbial communities. By targeting the 16S rRNA gene and internal transcribed spacer (ITS) region, we, respectively, described bacterial and fungal communities on eggshells of the homing pigeon Columba livia. We explored their structure, abundance, and composition. Firstly, we showed that sampling technique affected the outcome of the results. While broadly used, the egg swabbing procedure led to a lower DNA extraction efficiency and provided different profiles of bacterial communities than those based on crushed eggshell pieces. Secondly, we observed shifts in bacterial and fungal communities during incubation. At late incubation, bacterial communities showed a reduction in diversity, while their abundance increased, possibly due to the competitive advantage of some species. When compared to their bacterial counterparts, fungal communities also decreased in diversity at late incubation. In that case, however, the decline was associated with a diminution of their overall abundance. Conclusively, our results showed that although incubation might inhibit microbial growth when compared to unincubated eggs, we observed the selective growth of specific bacterial species during incubation. Moreover, we showed that fungi are a substantial component of the microbial communities associated with eggshells and require further investigations in avian ecology. Identifying the functional roles of these microorganisms is likely to provide news insights into the evolutionary strategies that control embryo survival.     

种植阔叶树种和毛竹对土壤有机碳矿化与微生物群落结构的影响

为探明种植阔叶树种和毛竹对土壤有机碳矿化与微生物群落特征的影响,本研究通过盆栽试验和室内培养法比较分析种植香樟、木荷、青冈等阔叶树种与毛竹的土壤有机碳矿化速率和累计矿化量,并结合末端限制性片段长度多态性(T-RFLP)以及荧光定量PCR技术,分析土壤细菌、真菌群落组分与数量特征.结果表明:与种植阔叶树种的土壤相比,种植...     

冻融对色季拉山高寒森林土壤微生物群落结构的影响

高寒森林土壤是最脆弱的陆地碳库之一,随着全球气候的变暖,冻融格局受到影响,这将导致土壤微生物群落结构发生变化进而影响土壤微生态过程。以西藏色季拉山不同海拔土壤为研究对象,基于16S rRNA测序技术探究微生物群落结构及多样性对季节性冻融的响应。结果表明:门水平上,冻融现象并未改变土壤细菌和真菌群落的优势菌群,变形菌门(Proteobacteria)、放线菌门(Actinobacteriota)和酸杆菌门(Acidobacteria)为细菌群落的优势菌门,担子菌门(Basidiomycota)和子囊菌门(Ascomycota)为真菌群落的优势菌门;属水平上,冻融前后微生物群落结构和组成差异较大,且细菌群落受冻融影响更剧烈,真菌群落受海拔影响更剧烈;OTU水平上,冻融使各海拔细菌群落和海拔3500 m、4300 m处真菌群落的α-多样性有较大提升,主要受黏粒和粉粒含量的影响;冻融使微生物群落组成在不同海拔间差异增大,且冻融前后的关键驱动因子不同,冻融前主要受碳氮比、速效钾、碳酸盐、土壤含水率、黏粒和粉粒含量的影响,冻融后主要受pH和有效磷的影响;相比于细菌,真菌群落结构的影响因素在海拔间的差异更大。本研究为深入理解气候暖化背景下不同海拔高寒森林土壤微生物对冻融的响应提供重要依据。     

Wide divergence of fungal communities inhabiting rocks and soils in a hyper-arid Antarctic desert

Highly simplified microbial communities colonise rocks and soils of continental Antarctica ice-free deserts. These two habitats impose different selection pressures on organisms, yet the possible filtering effects on the diversity and composition of microbial communities have not hitherto been fully characterised. We hence compared fungal communities in rocks and soils in three localities of inner Victoria Land. We found low fungal diversity in both substrates, with a mean species richness of 28 across all samples, and significantly lower diversity in rocks than in soils. Rock and soil communities were strongly differentiated, with a multinomial species classification method identifying just three out of 328 taxa as generalists with no affinity for either substrate. Rocks were characterised by a higher abundance of lichen-forming fungi (typically Buellia, Carbonea, Pleopsidium, Lecanora, and Lecidea), possibly owing to the more protected environment and the porosity of rocks permitting photosynthetic activity. In contrast, soils were dominated by obligate yeasts (typically Naganishia and Meyerozyma), the abundances of which were correlated with edaphic factors, and the black yeast Cryomyces. Our study suggests that strong differences in selection pressures may account for the wide divergences of fungal communities in rocks and soils of inner Victoria Land.     

葡萄生态系统中自然微生物群落多样性及其代谢酶系统的研究现状

自然微生物是影响葡萄生理生长和葡萄酒质量的重要因素,广泛存在于葡萄和葡萄酒的生态系统中。其中,微生物的种类、数量和生长分布取决于气候、土壤、生长时期和发酵过程控制等多种因素。自然状态下,葡萄微生态系统的物种组成和代谢作用直接影响葡萄藤的健康和葡萄酒的发酵质量,并产生特定的葡萄酒风土特征。因此,本文对现有研究的葡萄园土壤、果实和葡萄酒自然发酵过程中的真菌和细菌的群落多样性和动态变化,及其代谢酶类对葡萄酒质量特性的影响进行了综述,以期通过对微生物群落的生理代谢和生态作用的全面认识,探究葡萄微生态的互作机理和代谢功能,促使微生物群落向葡萄和葡萄酒有益的方向发展,从而达到葡萄生态系统可持续、高质量发展的目的。     

Importance of Saprotrophic Freshwater Fungi for Pollen Degradation

Fungi and bacteria are the major organic matter (OM) decomposers in aquatic ecosystems. While bacteria are regarded as primary mineralizers in the pelagic zone of lakes and oceans, fungi dominate OM decomposition in streams and wetlands. Recent findings indicate that fungal communities are also active in lakes, but little is known about their diversity and interactions with bacteria. Therefore, the decomposer niche overlap of saprotrophic fungi and bacteria was studied on pollen (as a seasonally recurring source of fine particulate OM) by performing microcosm experiments with three different lake types. Special emphasis was placed on analysis of fungal community composition and diversity. We hypothesized that (I) pollen select for small saprotrophic fungi and at the same time for typical particle-associated bacteria; (II) fungal communities form specific free-living and attached sub-communities in each lake type; (III) the ratio between fungi or bacteria on pollen is controlled by the lake''s chemistry. Bacteria-to-fungi ratios were determined by quantitative PCR (qPCR), and bacterial and fungal diversity were studied by clone libraries and denaturing gradient gel electrophoresis (DGGE) fingerprints. A protease assay was used to identify functional differences between treatments. For generalization, systematic differences in bacteria-to-fungi ratios were analyzed with a dataset from the nearby Baltic Sea rivers. High abundances of Chytridiomycota as well as occurrences of Cryptomycota and yeast-like fungi confirm the decomposer niche overlap of saprotrophic fungi and bacteria on pollen. As hypothesized, microbial communities consistently differed between the lake types and exhibited functional differences. Bacteria-to-fungi ratios correlated well with parameters such as organic carbon and pH. The importance of dissolved organic carbon and nitrogen for bacteria-to-fungi ratios was supported by the Baltic Sea river dataset. Our findings highlight the fact that carbon-to-nitrogen ratios may also control fungal contributions to OM decomposition in aquatic ecosystems.     

Plant traits determine the phylogenetic structure of arbuscular mycorrhizal fungal communities

Functional diversity in ecosystems has traditionally been studied using aboveground plant traits. Despite the known effect of plant traits on the microbial community composition, their effects on the microbial functional diversity are only starting to be assessed. In this study, the phylogenetic structure of arbuscular mycorrhizal (AM) fungal communities associated with plant species differing in life cycle and growth form, that is, plant life forms, was determined to unravel the effect of plant traits on the functional diversity of this fungal group. The results of the 454 pyrosequencing showed that the AM fungal community composition differed across plant life forms and this effect was dependent on the soil collection date. Plants with ruderal characteristics tended to associate with phylogenetically clustered AM fungal communities. By contrast, plants with resource‐conservative traits associated with phylogenetically overdispersed AM fungal communities. Additionally, the soil collected in different seasons yielded AM fungal communities with different phylogenetic dispersion. In summary, we found that the phylogenetic structure, and hence the functional diversity, of AM fungal communities is dependent on plant traits. This finding adds value to the use of plant traits for the evaluation of belowground ecosystem diversity, functions and processes.     

Influence of plant developmental stage on microbial community structure and activity in the rhizosphere of three field crops

Seasonal shifts in rhizosphere microbial populations were investigated to follow the influence of plant developmental stage. A field study of indigenous microbial rhizosphere communities was undertaken on pea (Pisum satvium var. quincy), wheat (Triticum aestivum var. pena wawa) and sugar beet (Beta vulgaris var. amythyst). Rhizosphere community diversity and substrate utilization patterns were followed throughout a growing season, by culturing, rRNA gene density gradient gel electrophoresis and BIOLOG. Culturable bacterial and fungal rhizosphere community densities were stable in pea and wheat rhizospheres, with dynamic shifts observed in the sugar beet rhizosphere. Successional shifts in bacterial and fungal diversity as plants mature demonstrated that different plants select and define their own functional rhizosphere communities. Assessment of metabolic activity and resource utilization by bacterial community-level physiological profiling demonstrated greater similarities between different plant species rhizosphere communities at the same than at different developmental stages. Marked temporal shifts in diversity and relative activity were observed in rhizosphere bacterial communities with developmental stage for all plant species studied. Shifts in the diversity of fungal and bacterial communities were more pronounced in maturing pea and sugar beet plants. This detailed study demonstrates that plant species select for specialized microbial communities that change in response to plant growth and plant inputs.