The rpb2 gene represents a viable alternative molecular marker for the analysis of environmental fungal communities

Although the commonly used internal transcribed spacer region of rDNA (ITS) is well suited for taxonomic identification of fungi, the information on the relative abundance of taxa and diversity is negatively affected by the multicopy nature of rDNA and the existence of ITS paralogues. Moreover, due to high variability, ITS sequences cannot be used for phylogenetic analyses of unrelated taxa. The part of single‐copy gene encoding the second largest subunit of RNA polymerase II (rpb2) was thus compared with first spacer of ITS as an alternative marker for the analysis of fungal communities in spruce forest topsoil, and their applicability was tested on a comprehensive mock community. In soil, rpb2 exhibited broad taxonomic coverage of the entire fungal tree of life including basal fungal lineages. The gene exhibited sufficient variation for the use in phylogenetic analyses and taxonomic assignments, although it amplifies also paralogues. The fungal taxon spectra obtained with rbp2 region and ITS1 corresponded, but sequence abundance differed widely, especially in the basal lineages. The proportions of OTU counts and read counts of major fungal groups were close to the reality when rpb2 was used as a molecular marker while they were strongly biased towards the Basidiomycota when using the ITS primers ITS1/ITS4. Although the taxonomic placement of rbp2 sequences is currently more difficult than that of the ITS sequences, its discriminative power, quantitative representation of community composition and suitability for phylogenetic analyses represent significant advantages.     

Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding

Freshwater fauna are particularly sensitive to environmental change and disturbance. Management agencies frequently use fish and amphibian biodiversity as indicators of ecosystem health and a way to prioritize and assess management strategies. Traditional aquatic bioassessment that relies on capture of organisms via nets, traps and electrofishing gear typically has low detection probabilities for rare species and can injure individuals of protected species. Our objective was to determine whether environmental DNA (eDNA) sampling and metabarcoding analysis can be used to accurately measure species diversity in aquatic assemblages with differing structures. We manipulated the density and relative abundance of eight fish and one amphibian species in replicated 206‐L mesocosms. Environmental DNA was filtered from water samples, and six mitochondrial gene fragments were Illumina‐sequenced to measure species diversity in each mesocosm. Metabarcoding detected all nine species in all treatment replicates. Additionally, we found a modest, but positive relationship between species abundance and sequencing read abundance. Our results illustrate the potential for eDNA sampling and metabarcoding approaches to improve quantification of aquatic species diversity in natural environments and point the way towards using eDNA metabarcoding as an index of macrofaunal species abundance.     

Community assembly after long-term fragmentation: a case study of tropical rainforest in Xishuangbanna,south-west China

Background: Tropical rainforests represent the most species-rich and at the same time the most fragmented terrestrial biome on Earth. Fragmentation of tropical rainforests is having wide-ranging consequences for the maintenance of local species diversity and community assembly patterns.

Aims: To examine floristic changes and changes in community phylogenetic structure in the forest fragment over the past five decades.

Methods: A new taxonomic diversity algorithm (within-family diversity) was developed to assess floristic changes in the forest fragment. Community phylogenetic structure was then compared before and after fragmentation.

Results: Taxonomic diversity changed greatly among families, with changes occurring randomly across the phylogeny. The forest fragment had higher phylogenetic diversity, higher mean pair-wise phylogenetic distance, but lower mean nearest-neighbour distance. The community phylogenetic structure has changed significantly from clustering to dispersion.

Conclusions: High species turnover occurred in the forest fragment. While shade-tolerant species have been lost, and ruderal and alien species have been added, overall phylogenetic diversity has increased with species being more phylogenetically distant. Competitive exclusion, which was related to the relatively drier conditions in the forest after fragmentation, led the plant community phylogenetic structure to be more dispersed.     

A time for every season: soil aggregate turnover stimulates decomposition and reduces carbon loss in grasslands managed for bioenergy

A primary goal of many next‐generation bioenergy systems is to increase ecosystem services such as soil carbon (C) storage and nutrient retention. Evaluating whether bioenergy management systems are achieving these goals is challenging in part because these processes occur over long periods of time at varying spatial scales. Investigation of microbially mediated soil processes at the microbe scale may provide early insights into the mechanisms driving these long‐term ecosystem services. Furthermore, seasonal fluctuations in microbial activity are rarely considered when estimating whole ecosystem functioning, but are central to decomposition, soil structure, and realized C storage. Some studies have characterized extracellular enzyme activity within soil structures (aggregates); however, seasonal variation in decomposition at the microscale remains virtually unknown, particularly in managed ecosystems. As such, we hypothesize that temporal variation in aggregate turnover is a strong regulator of microbial activity, with important implications for decomposition and C and nitrogen (N) storage in bioenergy systems. We address variation in soil microbial extracellular enzyme activity spatially across soil aggregates and temporally across two growing seasons in three ecosystems managed for bioenergy feedstock production: Zea mays L. (corn) agroecosystem, fertilized and unfertilized reconstructed tallgrass prairie. We measured potential N‐acetyl‐glucosaminidase (NAG), β‐glucosidase (BG), β‐xylosidase (BX), and cellobiohydrolase (CB) enzyme activity. Aggregate turnover in prairie systems was driven by precipitation events and seasonal spikes in enzyme activity corresponded with aggregate turnover events. In corn monocultures, soil aggregates turned over early in the growing season, followed by increasing, albeit low, enzyme activity throughout the growing season. Independent of management system or sampling date, NAG activity was greatest in large macroaggregates (>2000 μm) and CB activity was greatest in microaggregates (<250 μm). High microbial activity coupled with greater aggregation in prairie bioenergy systems may reduce loss of soil organic matter through decomposition and increase soil C storage.     

Plant and soil effects on bacterial communities associated with Miscanthus × giganteus rhizosphere and rhizomes

Bacterial assemblages, especially diazotroph assemblages residing in the rhizomes and the rhizosphere soil of Miscanthus × giganteus, contribute to plant growth and nitrogen use efficiency. However, the composition of these microbial communities has not been adequately explored nor have the potential ecological drivers for these communities been sufficiently studied. This knowledge is needed for understanding and potentially improving M. × giganteus – microbe interactions, and further enhancing sustainability of M. × giganteus production. In this study, cultivated M. × giganteus from four sites in Illinois, Kentucky, Nebraska, and New Jersey were collected to examine the relative influences of soil conditions and plant compartments on assembly of the M. × giganteus‐associated microbiome. Automated ribosomal intergenic spacer (ARISA) and terminal restriction fragment length polymorphism (T‐RFLP) targeting the nifH gene were applied to examine the total bacterial communities and diazotroph assemblages that reside in the rhizomes and the rhizosphere. Distinct microbial assemblages were detected in the endophytic and rhizosphere compartments. Site soil conditions had strong correlation with both total bacterial and diazotroph assemblages, but in different ways. Nitrogen treatments showed no significant effect on the composition of diazotroph assemblages in most sites. Endophytic compartments of different M. × giganteus plants tended to harbor similar microbial communities across all sites, whereas the rhizosphere soil of different plant tended to harbor diverse microbial assemblages that were distinct among sites. These observations offer insight into better understanding of the associative interactions between M. × giganteus and diazotrophs, and how this relationship is influenced by agronomic and edaphic factors.     

Specificity and localised distribution of mycorrhizal fungi in the soil may contribute to co-existence of orchid species

Co-occurring orchid species tend to occupy different areas and associate with different mycorrhizal fungi, suggesting that orchid mycorrhizal (OrM) fungi may be unevenly distributed within the soil and, therefore, impact the aboveground spatial distribution of orchids. To test this hypothesis, we investigated spatial variations in the community of potential OrM associates within the roots of three co-habitating orchid species (Anacamptis morio, Gymnadenia conopsea, and Orchis mascula) and the surrounding soil in an orchid-rich calcareous grassland in Southern Belgium using 454 amplicon pyrosequencing. Putative OrM fungi were broadly distributed in the soil, although variations in community composition were strongly related to the proximal host plant. The diversity and frequency of sequences corresponding to OrM fungi in the soil declined with increasing distance from orchid plants, suggesting that the clustered distribution of orchid species may to some extent be explained by the localised distribution of species-specific mycorrhizal associates.     

Cell‐to‐cell heterogeneity emerges as consequence of metabolic cooperation in a synthetic yeast community

Cells that grow together respond heterogeneously to stress even when they are genetically similar. Metabolism, a key determinant of cellular stress tolerance, may be one source of this phenotypic heterogeneity, however, this relationship is largely unclear. We used self‐establishing metabolically cooperating (SeMeCo) yeast communities, in which metabolic cooperation can be followed on the basis of genotype, as a model to dissect the role of metabolic cooperation in single‐cell heterogeneity. Cells within SeMeCo communities showed to be highly heterogeneous in their stress tolerance, while the survival of each cell under heat or oxidative stress, was strongly determined by its metabolic specialization. This heterogeneity emerged for all metabolite exchange interactions studied (histidine, leucine, uracil, and methionine) as well as oxidant (H₂O₂, diamide) and heat stress treatments. In contrast, the SeMeCo community collectively showed to be similarly tolerant to stress as wild‐type populations. Moreover, stress heterogeneity did not establish as sole consequence of metabolic genotype (auxotrophic background) of the single cell, but was observed only for cells that cooperated according to their metabolic capacity. We therefore conclude that phenotypic heterogeneity and cell to cell differences in stress tolerance are emergent properties when cells cooperate in metabolism.