Bacterial Dormancy Is More Prevalent in Freshwater than Hypersaline Lakes

Aanderud, Zachary T.; Vert, Joshua C.; Lennon, Jay T.; Magnusson, Tylan W.; Breakwell, Donald P.; Harker, Alan R.

doi:10.3389/fmicb.2016.00853

Cited by 46 publications

(27 citation statements)

References 104 publications

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“…Others studies based on RNA and DNA extractions have used the RNA/DNA ratio as a proxy to investigate microbial dormancy and to estimate the metabolically active community (Aanderud et al, 2016; Jones & Lennon, 2010). In a similar way we defined the root fungal microbiome of co-occurring A. stolonifera plants by combining the DNA- and RNA-based 18S rRNA amplicon analyses.…”

Section: Discussionmentioning

confidence: 99%

Ecophylogeny of the endospheric root fungal microbiome of co-occurring Agrostis stolonifera

Van

Quaiser

Duhamel

et al. 2017

PeerJ

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BackgroundWithin the root endosphere, fungi are known to be important for plant nutrition and resistance to stresses. However, description and understanding of the rules governing community assembly in the fungal fraction of the plant microbiome remains scarce.MethodsWe used an innovative DNA- and RNA-based analysis of co-extracted nucleic acids to reveal the complexity of the fungal community colonizing the roots of an Agrostis stolonifera population. The normalized RNA/DNA ratio, designated the ‘mean expression ratio’, was used as a functional trait proxy. The link between this trait and phylogenetic relatedness was measured using the Blomberg’s K statistic.ResultsFungal communities were highly diverse. Only ∼1.5% of the 635 OTUs detected were shared by all individuals, however these accounted for 33% of the sequence number. The endophytic fungal communities in plant roots exhibit phylogenetic clustering that can be explained by a plant host effect acting as environmental filter. The ‘mean expression ratio’ displayed significant but divergent phylogenetic signals between fungal phyla.DiscussionThese results suggest that environmental filtering by the host plant favours the co-existence of related and similar OTUs within the Basidiomycota community assembly, whereas the Ascomycota and Glomeromycota communities seem to be impacted by competitive interactions which promote the co-existence of phylogenetically related but ecologically dissimilar OTUs.

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Section: Discussionmentioning

confidence: 99%

Ecophylogeny of the endospheric root fungal microbiome of co-occurring Agrostis stolonifera

Van

Quaiser

Duhamel

et al. 2017

PeerJ

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“…Recent work has supported the existence of such microbial seed banks: For example, multiple studies have showed that the recruitment of rare bacteria can partly explain seasonal or spatial taxonomic changes within or across communities (Campbell et al, 2011;Sjöstedt et al, 2012;Caporaso et al, 2012a;Comte et al, 2014;Shade et al, 2014;Aanderud et al, 2015;Neuenschwander et al, 2015;Ruiz-González et al, 2015;Langenheder et al, 2016;Niño-García et al, 2016a). Other studies have considered the widespread dormancy found among bacteria or archaea (Jones and Lennon, 2010;Campbell et al, 2011;Hugoni et al, 2013;Aanderud et al, 2016) or the presence of core taxa that persist spatially and seasonally within or across habitat types (Caporaso et al, 2012a;Gibbons et al, 2013;Valter de Oliveira and Margis, 2015) as evidence of a seed bank. In spite of this evidence, the identification and delineation of the microbial seed bank remains difficult in practice.…”

Section: Introductionmentioning

confidence: 99%

Identifying the core seed bank of a complex boreal bacterial metacommunity

et al. 2017

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Seed banks are believed to contribute to compositional changes within and across microbial assemblages, but the application of this concept to natural communities remains challenging. Here we describe the core seed bank of a bacterial metacommunity from a boreal watershed, using the spatial distribution of bacterial operational taxonomic units (OTUs) across 223 heterogeneous terrestrial, aquatic and phyllosphere bacterial assemblages. Taxa were considered potential seeds if they transitioned from rare to abundant somewhere within the metacommunity and if they were ubiquitous and able to persist under unfavorable conditions, the latter assessed by checking their presence in three deeply sequenced samples (one soil, one river and one lake, 2.2-3 million reads per sample). We show that only a small fraction (13%) of all detected OTUs constitute a metacommunity seed bank that is shared between all terrestrial and aquatic communities, but not by phyllosphere assemblages, which seem to recruit from a different taxa pool. Our results suggest directional recruitment driven by the flow of water in the landscape, since most aquatic sequences were associated to OTUs found in a single deeply-sequenced soil sample, but only 45% of terrestrial sequences belonged to OTUs found in the two deeply-sequenced aquatic communities. Finally, we hypothesize that extreme rarity, and its interplay with water residence time and growth rates, may further constrain the size of the potential seed bank.

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“…In particular, pairing both 16S ribosomal transcripts (rRNA) as well as the 16S ribosomal gene (rDNA) sequencing allows for calculation of 16S rRNA:rDNA ratios, which attempts to normalize rRNA levels by the abundance of that taxon in the community and quantify its relative level of activity (8, 11, 14, 15). Taxa with 16S ratios greater than a specified threshold are considered ‘active’, and most studies report using a threshold of 1.0, which indicates more rRNA reads than rDNA reads for those taxa (6, 8, 16). One limitation to this approach is that using an arbitrary threshold to distinguish active from dormant taxa may be problematic in diverse communities (13, 17), given that rRNA production and growth rate are not necessarily always correlated (24–29).…”

Section: Introductionmentioning

confidence: 99%

16S rRNA:rDNA ratios and cell activity staining reveal consistent patterns of soil microbial activity

Bowsher

Kearns

Shade

2018

Preprint

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word count: 249 20 21 Article word count: 4351 (excluding Materials and Methods, References, and figure 22 legends) 23 2 24 25 Abstract 26Microbial activity plays a major role in the processes that support life on Earth. 27 Nevertheless, across diverse ecosystems many microbes are in a state of dormancy, 28 characterized by strongly reduced metabolic rates. Of the methods used to assess 29 microbial activity-dormancy dynamics, 16S rRNA: rDNA amplicons ("16S ratios") and 30 active cell staining with 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) are two of the 31 most common, yet each method has its own limitations. To better understand the 32 applicability and potential complementarity of these two methods, we conducted two 33 experiments investigating microbial activity in the rhizosphere. In the first experiment, 34 we treated corn rhizosphere soil with common phytohormones to simulate plant-soil 35 signaling during plant stress, and in the second experiment, we used bean exposed to 36 drought or nutrient enrichment to more directly assess the impacts of plant stress on soil 37 microbial activity. Overall, 16S ratios revealed numerous taxa with detectable RNA but 38 no detectable DNA. However, overarching patterns in percent activity across treatments 39 were unaffected by the method used to account for active taxa, or by the threshold 16S 40 ratio used for taxa to be classified as active. 16S ratio distributions were highly similar 41 across microbial phyla and were only weakly correlated with ribosomal operon number. 42 Lastly, over relatively short time courses, 16S ratios are responsive earlier than CTC 43 staining, a finding potentially related to the temporal sensitivity of activity changes 44 detectable by the two methods. Our results suggest that 16S ratios and CTC staining 45 provide robust and complementary estimates of bulk community activity.46 3 47 48 Although the majority of microorganisms in natural ecosystems are dormant, 49 relatively little is known about the dynamics of the active and dormant microbial pools 50 through both space and time. The limited knowledge of microbial activity-dormancy 51dynamics is in part due to uncertainty in the methods currently used to quantify active 52 taxa. Here, we directly compared two of the most common methods (16S ratios and 53 active cell staining) for estimating microbial activity in rhizosphere soil, and found that 54 they were largely in agreement in the overarching patterns, suggesting that either 55 method is robust for assessing comparative activity dynamics. Thus, our results suggest 56 that 16S ratios and active cell staining provide robust and complementary information 57 for measuring and interpreting microbial activity-dormancy dynamics in soils. They also 58 support that 16S rRNA:rDNA ratios have comparative value and offer a high-throughput, 59 sequencing-based option for understanding relative changes in microbiome activity.60 61 Keywords: 16S rRNA, 5-cyano-2,3-ditolyl tetrazolium chloride, dormancy, phantom 62 taxa 63 64 65 66 67 68 6...

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Bacterial Dormancy Is More Prevalent in Freshwater than Hypersaline Lakes

Cited by 46 publications

References 104 publications

Ecophylogeny of the endospheric root fungal microbiome of co-occurring Agrostis stolonifera

Ecophylogeny of the endospheric root fungal microbiome of co-occurring Agrostis stolonifera

Identifying the core seed bank of a complex boreal bacterial metacommunity

16S rRNA:rDNA ratios and cell activity staining reveal consistent patterns of soil microbial activity

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