Deterministic processes dominate nematode community structure in the Fynbos Mediterranean heathland of South Africa

Abstract

In many ecosystems, the factors that determine landscape-scale community structure of soil nematodes are poorly understood. We were interested in discovering whether deterministic or stochastic factors dominate nematode community variation. We used a novel metagenetic approach to investigate variation in nematode community structure in the Fynbos vegetation of South Africa. We compared 23 samples of soil nematode communities from five different Fynbos landscapes. Nematode DNA was 454-pyrosequenced for the 18S rRNA gene. We investigated the community structure, diversity, and the relative role of both deterministic (niche-based) and neutral processes may play in delimiting the nematode phylogenetic community structure in different Fynbos vegetation types. Nematode diversity showed no relationship to any measured soil parameter. The phylogenetic signal showed that more closely related types of nematodes in the Fynbos tended to co-occur more often than would be expected by chance, demonstrating that (a) closely related lineages occupy similar niches spatially and (b) community variation is influenced more by determinism than stochasticity. The standardised beta mean nearest taxon distance (ses.bMNTD) index showed no association with vegetation type. Both ses.NTI (nearest taxon index) and ses.bMNTD deviated significantly from null models, indicating that deterministic processes were important in the assembly of nematode communities. Furthermore, at local scale, the ses.NTI was significantly higher than Electronic supplementary material The online version of this article (null expectations, indicating that co-occurrence of related nematode lineages is determined by the differences in environmental conditions across the sites. We conclude that in the Fynbos there is niche overlap between closely related types of nematodes, that nematode speciation tends to occur conservatively into closely related niches, and that the phylogenetic community structure reveals that deterministic (rather than stochastic) processes are more important in delimiting the community assembly.

Distinct assembly mechanisms underlie similar biogeographical patterns of rare and abundant bacteria in Tibetan Plateau grassland soils

“…Phylogeny-based community metrics, such as the β-mean nearest taxon distance (β-MNTD) and UniFrac distance, are receiving increased attention (Lozupone et al, 2011;Stegen et al, 2012). Compared with composition-based community metrics, these phylogenybased community metrics can be used to infer changes in microbial community function (Stegen et al, 2013;Dini-Andreote et al, 2015;Moroenyane et al, 2016). This is based on the assumption that phylogenetically closerelated microorganisms have similar habitat associations (Stegen et al, 2012).…”

Functional Diversity of Soil Nematodes in Relation to the Impact of Agriculture—A Review

“…The soil spatial heterogeneity and the temporal variation in resource availability create high microhabitat diversity, potential for resource utilization and niche partitioning, and hence complex biotic interactions. In natural systems, deterministic (i.e., niche-based) rather than stochastic processes were found to be more important in delimiting the phylogenetic nematode community structure [54]. Closely related nematode phylotypes tended to co-occur more often, demonstrating that closely related lineages occupy similar niches.…”

Distinct assembly mechanisms underlie similar biogeographical patterns of rare and abundant bacteria in Tibetan Plateau grassland soils

“…Composition-based metrics have traditionally been used to examine microbial community structure variations, but phylogeny-based community metrics, such as the β-mean nearest taxon distance (β-MNTD) and UniFrac distance, are receiving increased attention [19,20]. Compared to compositionbased community metrics, these phylogeny-based community metrics can be used to infer changes in microbial community function [21][22][23]. This is based on the assumption that phylogenetically close-related microorganisms have similar habitat associations [20].…”