Forests are essential biomes for global biogeochemical cycles, and belowground microorganisms have a key role in providing relevant ecosystem services. To predict the effects of environmental changes on these ecosystem services requires a comprehensive understanding of how biotic and abiotic factors drive the composition of microbial communities in soil. However, microorganisms are not homogeneously distributed in complex environments such as soil, with different features affecting microbes at different extent depending on the niche they occupy. Indeed, this spatial heterogeneity hampers the extrapolation of microbial diversity study results from particular habitats to the ecosystem level, even if the resolution of the more recent studies has increased significantly after the standardization of high-throughput sequencing techniques. The present work intends to give a comprehensive view of the knowledge accumulated until date defining the more important drivers determining the structure of forest soil microbial communities from fine to continental scales.

• Klíčová slova
• Community structure, Drivers, Forest, Microbial diversity, Soil,
• MeSH
• Bacteria MeSH
• ekosystém * MeSH
• lesy * MeSH
• mikrobiota fyziologie   MeSH
• půda chemie   MeSH
• půdní mikrobiologie * MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• půda MeSH

Nutrient addition may change soil microbial community structure, but soil microbes must simultaneously contend with other, interacting factors. We studied the effect of soil type (peat, mineral), water level (low, high), and nutrient addition (unfertilized, fertilized) on wet grassland soil microbial community structure in both vegetated and un-vegetated soils after five years of treatment application in a mesocosm, using Illumina sequencing of the bacterial V4 region of the small ribosomal sub-units. Soil type, water level, and plant presence significantly affected the soil microbial structure, both singly and interactively. Nutrient addition did not directly impact microbiome structure, but acted indirectly by increasing plant biomass. The abundance of possible plant growth promoting bacteria and heterotrophic bacteria indicates the importance of bacteria that promote plant growth. Based on our results, a drier and warmer future would result in nutrient-richer conditions and changes to microbial community structure and total microbial biomass and/or abundances, with wet grasslands likely switching from areas acting as C sinks to C sources.

• Klíčová slova
• Carex acuta, context dependence, r/K strategies, soil microbial community structure, wet grasslands,
• MeSH
• Bacteria MeSH
• biomasa MeSH
• mikrobiota * MeSH
• pastviny * MeSH
• půda chemie   MeSH
• půdní mikrobiologie MeSH
• rostliny mikrobiologie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• půda MeSH

Feedstock type influences bacterial and methanogenic communities in anaerobic digestion. These two communities work tightly to maintain the stability of anaerobic digestion. How to quick report the changes of microbial community structure especially methanogenesis is the key issue for optimizing anaerobic digestion process. In this study, 13C isotope fractionations of CH4 and CO2 in biogas and microbial community composition were analyzed in 5 different feedstocks. Our results showed that grass silage, maize silage and swine manure fed reactors had similar δ 13C values and methanogenic community composition, dominated by Methanosarcinaceae. The lowest δ 13CH4 values were detected in straw and chicken manure fed reactors, reflecting reduced microbial degradation of material or the presence of toxic components in these feedstocks. The straw fed bioreactor lead to low δ 13CH4 values, probably reflecting relatively high levels of the syntrophic acetate oxidizing bacteria, Synergistaceae and Syntrophaceae, which might work collectively with hydrogenotrophic methanogens, resulting in the low δ 13CH4 values in this bioreactor. Significantly, all core microbes in the 5 different feedstock fed bioreactors were either Clostridia species or related to the Synergistaceae (syntrophic acetate oxidizing bacteria).

• Klíčová slova
• Anaerobic digestion, Bacterial community, Feedstock, Isotope fractionation, Methanogenesis,
• MeSH
• anaerobióza MeSH
• biopaliva * MeSH
• bioreaktory MeSH
• hnůj MeSH
• izotopy MeSH
• methan MeSH
• mikrobiota * MeSH
• prasata MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• biopaliva * MeSH
• hnůj MeSH
• izotopy MeSH
• methan MeSH

Potato scab is a common potato tuber disease that affects quality and cost in the marketplace, shortening storage, and increasing the chance for secondary infection. The tubers with disease severity of 1 to 4 are accepted and stored in potato storage for cheap selling in Thailand. However, there are few studies of the bacterial community of the scabby tuber during storage. Thus, we aim to elucidate the diversity, structure, and function of the bacterial community of 30-day storage potato scabby tubers stored in different temperatures using 16S amplicon metagenomic sequencing. Bacterial communities of storage potato scabby tubers (Spunta cultivar) collected from different storage temperatures, 4 °C (MEP1) and 6 °C (MEP2), were characterized using 16S rRNA amplicon metagenomic sequencing. The alpha-diversity abundance in the bacteriome of the scabby tubers stored at 6 °C was higher than in those stored at 4 °C. Actinobacteria (34.7%) was a dominant phylum in MEP1, while Proteobacteria (39.9%) was predominant in MEP2. The top 10 genera of both communities were Rhizobium group, Streptomyces, Pectobacterium, Ruminococcus, Cellulomonas, Promicromonospora, Prevotella, Enterobacter, Pedobacter, and Paenarthrobacter. Moreover, functional profile prediction of both communities reveals essential genes in the pathosystem: nos, bglA, and cebEFG-msiK for potato scab disease and phc and peh operons for rot disease. Our findings are the first study to explore details of the bacteriome of the accepted potato scabby tubers for selling during storage in Thailand and strongly indicate that although potatoes were stored at low temperatures, diseases still occur by secondary pathogens.

• Klíčová slova
• Amplicon metagenomic sequencing, Bacterial community structure, Bacterial diversity, Functional gene profile, Plant pathogenic bacteria, Potato scabby tubers,
• MeSH
• Bacteria * genetika   klasifikace   izolace a purifikace   MeSH
• biodiverzita MeSH
• DNA bakterií genetika   MeSH
• fylogeneze MeSH
• hlízy rostlin * mikrobiologie   MeSH
• metagenomika MeSH
• mikrobiota MeSH
• nemoci rostlin * mikrobiologie   MeSH
• RNA ribozomální 16S * genetika   MeSH
• skladování potravin * MeSH
• Solanum tuberosum * mikrobiologie   MeSH
• teplota MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Thajsko MeSH
• Názvy látek
• DNA bakterií MeSH
• RNA ribozomální 16S * MeSH

The spatial distributions of bacteria in the soil matrix have a role in ecosystem function, for example, at the small scale, through gene transfer or xenobiotic degradation. Soil bacterial biogeography has been evidenced at the large scale, but data are scarce at the small scale. The objective of this work was to determine the spatial pattern of bacterial diversity, in spatially referenced microsamples, in order to define bacterial community spatial traits. Two soils with different physical structures, moderately aggregated (La Côte St André (LCSA)) or poorly aggregated (La Dombes (LD)), were studied. The spatial distribution of bacteria was studied in microsamples (diameter 3 mm) along 10- and 20-cm transects, with a taxonomic microarray. 16S rRNA gene sequencing was used to further study the spatial characteristics of the microbial communities in LD soil. The frequency-occupancy plot, in the LCSA and LD soils, using microarray and sequencing data, followed Hanski's core-satellite theory. The frequency-occupancy distribution plots obtained in two different soils showed bimodality and indicated that the microscale spatial distributions were different, particularly core taxa percentage. Core taxa are widespread and abundant, while satellite taxa are restricted in their distribution. The spread of satellite taxa was at a distance range larger than 5 cm, whereas the core taxa were distributed in a distance range less than 3 mm. Besides, there was a positive abundancy-occupancy relationship at this fine scale. It may be interesting to further evaluate the role of the different bacterial spatial distributions at the fine scale on soil function.

• Klíčová slova
• Abundancy-occupancy relationship, Bacteria community structure, Frequency-occupancy relationship, Microscale in soil, Soil microbial diversity, Soil structure,
• MeSH
• Bacteria klasifikace   genetika   MeSH
• biodiverzita * MeSH
• DNA bakterií MeSH
• ekosystém MeSH
• molekulární typizace MeSH
• půda chemie   MeSH
• půdní mikrobiologie * MeSH
• RNA ribozomální 16S genetika   MeSH
• sekvence nukleotidů MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Francie MeSH
• Názvy látek
• DNA bakterií MeSH
• půda MeSH
• RNA ribozomální 16S MeSH

BACKGROUND: Localised patterns of species diversity can be influenced by many factors, including regional species pools, biogeographic features and interspecific interactions. Despite recognition of these issues, we still know surprisingly little about how invertebrate biodiversity is structured across geographic scales. In particular, there have been few studies of how insect communities vary geographically while using the same plant host. We compared the composition (species, genera) and functional structure (guilds) of the chalcid wasp communities associated with the widespread fig tree, Ficus benjamina, towards the northern (Hainan province, China) and southern (Queensland, Australia) edges of its natural range. Sequence data were generated for nuclear and mtDNA markers and used to delimit species, and Bayesian divergence analyses were used to test patterns of community cohesion through evolutionary time. RESULTS: Both communities host at least 14 fig wasp species, but no species are shared across continents. Community composition is similar at the genus level, with six genera shared although some differ in species diversity between China and Australia; a further three genera occur in only China or Australia. Community functional structure remains very similar in terms of numbers of species in each ecological guild despite community composition differing a little (genera) or a lot (species), depending on taxonomic level. Bayesian clustering analyses favour a single community divergence event across continents over multiple events for different ecological guilds. Molecular dating estimates of lineage splits between nearest inter-continental species pairs are broadly consistent with a scenario of synchronous community divergence from a shared "ancestral community". CONCLUSIONS: Fig wasp community structure and genus-level composition are largely conserved in a wide geographic comparison between China and Australia. Moreover, dating analyses suggest that the functional community structure has remained stable for long periods during historic range expansions. This suggests that ecological interactions between species may play a persistent role in shaping these communities, in contrast to findings in some comparable temperate systems.

• Klíčová slova
• Barcoding, Biodiversity, Chalcidoidea, Community composition, Ficus, Galler, Parasitoid, Wasp,
• MeSH
• biologická evoluce * MeSH
• Ficus růst a vývoj   MeSH
• fylogeneze MeSH
• hmyzí proteiny analýza   MeSH
• mezerníky ribozomální DNA analýza   MeSH
• potravní řetězec * MeSH
• respirační komplex IV analýza   MeSH
• sekvenční analýza DNA MeSH
• společenstvo * MeSH
• sršňovití genetika   fyziologie   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Austrálie MeSH
• Čína MeSH
• Názvy látek
• hmyzí proteiny MeSH
• mezerníky ribozomální DNA MeSH
• respirační komplex IV MeSH

Plant-microbe interactions are of particular importance in polluted soils. This study sought to determine how selected plants (horseradish, black nightshade and tobacco) and NPK mineral fertilization shape the structure of soil microbial communities in legacy contaminated soil and the resultant impact of treatment on the soil microbial community functional potential. To explore these objectives, we combined shotgun metagenomics and 16S rRNA gene amplicon high throughput sequencing with data analysis approaches developed for RNA-seq. We observed that the presence of any of the selected plants rather than fertilization shaped the microbial community structure, and the microbial populations of the root zone of each plant significantly differed from one another and/or from the bulk soil, whereas the effect of the fertilizer proved to be insignificant. When we compared microbial diversity in root zones versus bulk soil, we observed an increase in the relative abundance of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria or Bacteroidetes, taxa which are commonly considered copiotrophic. Our results thus align with the theory that fast-growing, copiotrophic, microorganisms which are adapted to ephemeral carbon inputs are enriched in the vegetated soil. Microbial functional potential indicated that some genetic determinants associated with signal transduction mechanisms, defense mechanisms or amino acid transport and metabolism differed significantly among treatments. Genetic determinants of these categories tend to be overrepresented in copiotrophic organisms. The results of our study further elucidate plant-microbe relationships in a contaminated environment with possible implications for the phyto/rhizoremediation of contaminated areas.

• Klíčová slova
• contaminated soil, fertilization, functional potential, microbial community structure, plants,
• Publikační typ
• časopisecké články MeSH

Orchid mycorrhizal (OrM) fungi play a crucial role in the ontogeny of orchids, yet little is known about how the structure of OrM fungal communities varies with space and environmental factors. Previous studies suggest that within orchid patches, the distance to adult orchids may affect the abundance of OrM fungi. Many orchid species grow in species-rich temperate semi-natural grasslands, the persistence of which depends on moderate physical disturbances, such as grazing and mowing. The aim of this study was to test whether the diversity, structure and composition of OrM fungal community are influenced by the orchid patches and management intensity in semi-natural grasslands. We detected putative OrM fungi from 0 to 32 m away from the patches of host orchid species (Orchis militaris and Platanthera chlorantha) in 21 semi-natural calcareous grasslands using pyrosequencing. In addition, we assessed different ecological conditions in semi-natural grasslands but primarily focused on the effect of grazing intensity on OrM fungal communities in soil. We found that investigated orchid species were mostly associated with Ceratobasidiaceae and Tulasnellaceae and, to a lesser extent, with Sebacinales. Of all the examined factors, the intensity of grazing explained the largest proportion of variation in OrM fungal as well as total fungal community composition in soil. Spatial analyses showed limited evidence for spatial clustering of OrM fungi and their dependence on host orchids. Our results indicate that habitat management can shape OrM fungal communities, and the spatial distribution of these fungi appears to be weakly structured outside the orchid patches.

• Klíčová slova
• Calcareous grassland, Fungal community composition, Grazing intensity, Next-generation sequencing, Orchid mycorrhiza, Spatial distribution,
• MeSH
• Basidiomycota MeSH
• fylogeneze MeSH
• mykorhiza klasifikace   MeSH
• Orchidaceae mikrobiologie   MeSH
• pastviny * MeSH
• půdní mikrobiologie * MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Estonsko MeSH

Variation along environmental gradients in host-associated microbial communities is not well understood compared to free-living microbial communities. Because elevational gradients may serve as natural proxies for climate change, understanding patterns along these gradients can inform our understanding of the threats hosts and their symbiotic microbes face in a warming world. In this study, we analyzed bacterial microbiomes from pupae and adults of four Drosophila species native to Australian tropical rainforests. We sampled wild individuals at high and low elevations along two mountain gradients to determine natural diversity patterns. Further, we sampled laboratory-reared individuals from isofemale lines established from the same localities to see if any natural patterns are retained in the lab. In both environments, we controlled for diet to help elucidate other deterministic patterns of microbiome composition. We found small but significant differences in Drosophila bacterial community composition across elevation, with some notable taxonomic differences between different Drosophila species and sites. Further, we found that field-collected fly pupae had significantly richer microbiomes than laboratory-reared pupae. We also found similar microbiome composition in both types of provided diet, suggesting that the significant differences found among Drosophila microbiomes are the products of surrounding environments with different bacterial species pools, possibly bound to elevational differences in temperature. Our results suggest that comparative studies between lab and field specimens help reveal the true variability in microbiome communities that can exist within a single species. IMPORTANCE Bacteria form microbial communities inside most higher-level organisms, but we know little about how the microbiome varies along environmental gradients and between natural host populations and laboratory colonies. To explore such effects on insect-associated microbiomes, we studied the gut microbiome in four Drosophila species over two mountain gradients in tropical Australia. We also compared these data to individuals kept in the laboratory to understand how different settings changed microbiome communities. We found that field-sampled individuals had significantly higher microbiome diversity than those from the lab. In wild Drosophila populations, elevation explains a small but significant amount of the variation in their microbial communities. Our study highlights the importance of environmental bacterial sources for Drosophila microbiome composition across elevational gradients and shows how comparative studies help reveal the true flexibility in microbiome communities that can exist within a species.

• Klíčová slova
• Drosophila, bacteria, community, ecology, elevation gradient, field and laboratory, metabarcoding, microbiome, symbiosis,
• MeSH
• Bacteria genetika   MeSH
• Drosophila mikrobiologie   MeSH
• mikrobiota * MeSH
• střevní mikroflóra * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Austrálie MeSH

Important functions of constructed wetland related to biogeochemical processes are mediated by soil microbes and low-temperature damage is the main limiting factor for microbes in winter. However, the response thresholds for active microbial community and enzyme activities to continuous decreases in temperature remain unclear. In this study, total 90 soil samples were collected every week over a 6-week period to track the dynamics of four enzymes involved in cycles of C, N, P and active bacterial community as field soil temperature decreased continuously from 6.62 °C to 0.55 °C. Enzyme activity changed suddenly when the temperature decreased to 4.83 °C, the nitrite reductase activity reduced by 36.2%, while alkaline phosphatase activity is increased by 396%. The cellulase and urease were only marginally influenced by cold stress. Decreased nitrite reductase activities corresponded with loss of nir-type denitrifiers important for nitrite reduction. For cold stress, N-related bacteria were sensitive species. Whereas increased alkaline phosphatase activity may be due to the fact that P-related bacteria were opportunistic species. Key functional taxa connected with degradation of cellulose promoted species coexistence and microbial network stability. The lower and upper temperature thresholds for community change were 4.85 °C and 6.30 °C, respectively. Collectively, these results revealed that microbial taxa involved in C, N and P cycling respond differently to continuous decreases in temperature and higher than 4.85 °C is an ideal environment to prevent loss of microbial diversity and functions in winter, providing a scientific reference for the targeted isolation and cultivation of key microbial taxa in rhizosphere soil and adjusting temperature range to improve the purification capacity of wetlands during low temperature periods.

• Klíčová slova
• Active bacterial community, Constructed wetland, Continuous decreases in temperature, Enzyme dynamics, Rhizosphere soil, Winter,
• MeSH
• alkalická fosfatasa metabolismus   MeSH
• Bacteria metabolismus   MeSH
• mikrobiota * MeSH
• mokřady * MeSH
• nitritreduktasy metabolismus   MeSH
• půda chemie   MeSH
• půdní mikrobiologie MeSH
• teplota MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• alkalická fosfatasa MeSH
• nitritreduktasy MeSH
• půda MeSH