The gastrointestinal tracts of animals contain diverse communities of microbes that provide a number of services to their hosts. There is recent concern that these communities may be lost as animals enter captive breeding programmes, due to changes in diet and/or exposure to environmental sources. However, empirical evidence documenting the effects of captivity and captive birth on gut communit...

The site-to-site variability in species composition, known as β-diversity, is crucial to understanding spatiotemporal patterns of species diversity and the mechanisms controlling community composition and structure. However, quantifying β-diversity in microbial ecology using sequencing-based technologies is a great challenge because of a high number of sequencing errors, bias, and poor reproduc...

The microbial genome database for comparative analysis (MBGD, available at http://mbgd.genome.ad.jp/) is a platform for microbial genome comparison based on orthology analysis. As its unique feature, MBGD allows users to conduct orthology analysis among any specified set of organisms; this flexibility allows MBGD to adapt to a variety of microbial genomic study. Reflecting the huge diversity of...

Understanding the effects of environmental factors on microbial communities is critical for microbial ecology, but it remains challenging. In this study, we examined the diversity (alpha diversity) and community compositions (beta diversity) of prokaryotes and fungi in hypersaline sediments and salinized soils from northern China. Environmental variables were highly correlated, but they differe...

The role of macrobiota in structuring microbial communities along rocky shores. PeerJ 2:e631 Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was signifi...

Arid ecosystems are characterized by high spatial heterogeneity, and the variation among vegetation patches is a clear example. Soil biotic and abiotic factors associated with these patches have also been well documented as highly heterogeneous in space. Given the low vegetation cover and little precipitation in arid ecosystems, soil microorganisms are the main drivers of nutrient cycling. None...

Plants and insects have been co-existing for more than 400 million years, leading to intimate and complex relationships. Throughout their own evolutionary history, plants and insects have also established intricate and very diverse relationships with microbial associates. Studies in recent years have revealed plant- or insect-associated microbes to be instrumental in plant-insect interactions, ...

To understand how contaminants affect microbial community diversity, heterogeneity, and functional structure, six groundwater monitoring wells from the Field Research Center of the U.S. Department of Energy Environmental Remediation Science Program (ERSP; Oak Ridge, TN), with a wide range of pH, titrate, and heavy metal contamination were investigated. DNA from the groundwater community was ana...

Grassland managements can affect carbon (C) and nitrogen (N) storage in grassland ecosystems with consequent feedbacks to climate change. We investigated the impacts of compound fertilization and clipping on grass biomass, plant and soil (0-20 cm depth) C, N storage, plant and soil C: N ratios, soil microbial activity and diversity, and C, N sequestration rates in grassland in situ in the Natio...

The sulfate-methane transition zone (SMTZ) is a widespread feature of continental margins, representing a diffusion-controlled interface where there is enhanced microbial activity. SMTZ microbial activity is commonly associated with the anaerobic oxidation of methane (AOM), which is carried out by syntrophic associations between sulfate-reducing bacteria and methane-oxidizing archaea. While our...