Habitat generalists and specialists in microbial communities across a terrestrial-freshwater gradient

Abstract

Observations of distributions of microorganisms and their differences in community composition across habitats provide evidence of biogeographical patterns. However, little is known about the processes controlling transfers across habitat gradients. By analysing the overall microbial community composition (bacteria, fungi, archaea) across a terrestrial-freshwater gradient, the aim of this study was to understand the spatial distribution patterns of populations and identify taxa capable of crossing biome borders. Barcoded 454 pyrosequencing of taxonomic gene markers was used to describe the microbial communities in adjacent soil, freshwater and sediment samples and study the role of biotic and spatial factors in shaping their composition. Few habitat generalists but a high number of specialists were detected indicating that microbial community composition was mainly regulated by species sorting and niche partitioning. Biotic interactions within microbial groups based on an association network underlined the importance of Actinobacteria, Sordariomycetes, Agaricomycetes and Nitrososphaerales in connecting among biomes. Even if dispersion seemed limited, the shore of the lake represented a transition area, allowing populations to cross the biome boundaries. In finding few broadly distributed populations, our study points to biome specialization within microbial communities with limited potential for dispersal and colonization of new habitats along the terrestrial-freshwater continuum.

Toward more robust plant‐soil feedback research

“…This is not a trivial assumption: Mounting evidence indicates soil biota compositions vary widely across small spatial scales due to dispersal processes, soil physicochemical properties, soil water content, and other factors (Monard et al 2016, Zhang et al 2016, Ping et al 2017, Seuradge et al 2017). This is not a trivial assumption: Mounting evidence indicates soil biota compositions vary widely across small spatial scales due to dispersal processes, soil physicochemical properties, soil water content, and other factors (Monard et al 2016, Zhang et al 2016, Ping et al 2017, Seuradge et al 2017).…”

“…Combining soil samples by NAS and species prevented Teste et al from confirming step 1. Soil microbe compositions can vary widely across small spatial scales (Monard et al 2016, Zhang et al 2016, Ping et al 2017, Seuradge et al 2017, Wang et al 2017, so some sampled microbial species may have occurred near just one or a few field plants. Even microbes occurring near a single plant would presumably be distributed to 20 conspecific glasshouse pots and ≥150 NAS mixture pots (Appendix S1: Fig.…”

“…In order to conclude that phytometers grown in unconditioned field soil measure PSFs occurring in nature, it must be assumed that field plants causally determine which soil biota occur where. This is not a trivial assumption: Mounting evidence indicates soil biota compositions vary widely across small spatial scales due to dispersal processes, soil physicochemical properties, soil water content, and other factors (Monard et al 2016, Zhang et al 2016, Ping et al 2017, Seuradge et al 2017, Wang et al 2017). Insofar as stochastic or abiotic factors determine which soil biota occur where, phytometers will be misleading indicators of PSFs.…”

Metabolic insight into bacterial community assembly across ecosystem boundaries

“…Dispersing across an ecosystem boundary is likely a harsh transition for many bacteria (Monard et al 2016). Although most active aquatic taxa were also detected in nearby soils, only a minority of taxa present in soils were common in the active aquatic community (Fig.…”

Analysis of single-cell genome sequences of bacteria and archaea

“…Since the development of molecular-based, cultivation-independent tools, we have witnessed a burst in the detection of previously elusive microbial taxa. This was initially driven by the widespread adoption of high-throughput 16S rRNA gene sequencing where studies now span ecological gradients [1] and, in some cases, cross-biome comparisons [2,3]. However, 16S rRNA gene PCR-based surveys are limited due to constraints inherent to single-gene surveys.…”