Biological invasions alter environmental microbiomes: a meta-analysis

Malacrinò, Antonino; Sadowski, Victoria A; Martin, Tvisha; Oliveira, Nathalia Cavichiolli de; Brackett, Ian J.; Feller, James D.; Harris, Kira; COMBITA-HEREDIA, ORLANDO; Vescio, Rosa; Bennett, Alison E.

doi:10.1101/2020.06.17.157883

Cited by 2 publications

(1 citation statement)

References 83 publications

(86 reference statements)

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“…In our study, rather than considering optimal phylogenetic placement as above, we have focused on an alternative taxonomic approach to give reasonable resolution of species. A phylogenetic tree is necessary as it allows for a deeper understanding of the microbial community relationships and microbial community assembly processes [7], [10], [11]. In complex microbial systems such as wastewater treatment biofilms large-scale understanding of ecosystem function and taxa interaction through phylogenetic statistical analysis have the potential to unlock our ability to control or manipulate the community [12].…”

Section: Introductionmentioning

confidence: 99%

Circular Economy of Anaerobic Biofilm Microbiomes: A Meta-Analysis Framework for Re-exploration of Amplicon Sequencing Data

Keating

Trego

Sloan

et al. 2020

Preprint

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Use of high-throughput sequencing is widespread in efforts to understand the microbial communities in natural and engineered systems. Many built ecosystems, in particular those used for engineered wastewater treatment, have harnessed the metabolic capacity of complex microbial communities for the effective removal and recovery of organic pollutants. Recent efforts to better understand and precisely engineer such systems have increasingly used high-throughput sequencing to map the structure and function of wastewater treatment microbiomes. An enormous amount of data is readily available on online repositories such as the National Center for Biotechnology Information Short Read Archive (NCBI SRA). Here, we describe and provide an optimised meta-analysis workflow to utilise this resource to collate heterogenous studies together for anaerobic digestion research. We analysed 16S rRNA gene Illumina Miseq amplicon sequencing data from 31 anaerobic digestion studies (from high-rate digesters), including >1,300 samples. Additionally, we compare several methodological choices: extraction method, v-region, taxonomical database, and the classifier. We demonstrate that collation of data from multiple v-regions can be achieved by using only the taxa for which sequences are available in the reference databases, without losses in diversity trends. This is made possible by focusing on alternative strategies for taxonomic assignments, namely, bayesian lowest common ancestor (BLCA) algorithm which offers increased resolution to the traditional naïve bayesian classifier (NBC). While we demonstrate this using an anaerobic digestion wastewater treatment dataset, this methodology can be translated to perform meta-analysis on amplicon sequences in any field. These findings not only provide a roadmap for meta-analysis in any field, but additionally provide an opportunity to reuse extensive data resources to ultimately advance knowledge of wastewater treatment systems.ImportanceIn this study, we have combined sequencing data from 31 individual studies with the purpose of identifying a meta-analysis workflow which can accurately collate data derived from sequencing different v-regions with minimal data loss and more accurate diversity patterns. While we have used Anaerobic Digestion (AD) communities for our proof-of-concept, our workflow (Fig 1) can be translated to any Illumina MiSeq meta-analysis study, in any field. Thereby, we provide the foundation for intensive data mining of existing amplicon sequencing resources. Such data-mining can provide a global perspective on complex microbial communities.Graphical Abstract

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Section: Introductionmentioning

confidence: 99%

Circular Economy of Anaerobic Biofilm Microbiomes: A Meta-Analysis Framework for Re-exploration of Amplicon Sequencing Data

Keating

Trego

Sloan

et al. 2020

Preprint

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Spatial Diversity in Bacterial Communities across Barren and Vegetated, Native and Invasive, Coastal Dune Microhabitats

2021

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The microbial community composition of coastal dunes can vary across environmental gradients, with the potential to impact erosion and deposition processes. In coastal foredunes, invasive plant species establishment can create and alter environmental gradients, thereby altering microbial communities and other ecogeomorphic processes with implications for storm response and management and conservation efforts. However, the mechanisms of these processes are poorly understood. To understand how changing microbial communities can alter these ecogeomorphic dynamics, one must first understand how soil microbial communities vary as a result of invasion. Towards this goal, bacterial communities were assessed spatially along foredune microhabitats, specifically in barren foredune toe and blowout microhabitats and in surrounding vegetated monocultures of native Ammophila breviligulata and invasive Carex kobomugi. Across dune microhabitats, microbial composition was more dissimilar in barren dune toe and blowout microhabitats than among the two plant species, but it did not appear that it would favor the establishment of one plant species over the other. However, the subtle differences between the microbial community composition of two species could ultimately aid in the success of the invasive species by reducing the proportions of bacterial genera associated exclusively with A. breviligulata. These results suggest that arrival time may be crucial in fostering microbiomes that would further the continued establishment and spread of either plant species.

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Biological invasions alter environmental microbiomes: a meta-analysis

Cited by 2 publications

References 83 publications

Circular Economy of Anaerobic Biofilm Microbiomes: A Meta-Analysis Framework for Re-exploration of Amplicon Sequencing Data

Circular Economy of Anaerobic Biofilm Microbiomes: A Meta-Analysis Framework for Re-exploration of Amplicon Sequencing Data

Spatial Diversity in Bacterial Communities across Barren and Vegetated, Native and Invasive, Coastal Dune Microhabitats

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