Biology subjects

Lindh, M. V.

Publications and source records attributed to Lindh, M. V..

3 recordsLinked to original sources

bioRxiv2017

Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes

BackgroundProkaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms.\n\nResultsWe compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (>98.7% identity) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs; the metagenome assembly was found to cause incompleteness to a higher degree than the binning procedure.\n\nConclusionsThe strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.

bioinformatics↗

bioRxiv2017

Defining Marine Microbial Biomes From Environmental And Dispersal Filtered Metapopulations

Energy and matter fluxes essential for all life1 are modulated by spatial and temporal shifts in microbial community structure resulting from environmental and dispersal filtering2,3, emphasizing the continued need to characterize microbial biogeography4,5. Yet, application of metapopulation theory, traditionally used in general ecology for understanding shifts in biogeographical patterns among macroorganisms, has not been tested extensively for defining marine microbial populations filtered by environmental conditions and dispersal limitation at global ocean scales. Here we show, from applying metapopulation theory on two major global ocean datasets6,7, that microbial populations exhibit core- and satellite distributions with cosmopolitan compared to geographically restricted distributions of populations. We found significant bimodal occupancy-frequency patterns (the different number of species occupying different number of patches) at varying spatial scales, where shifts from bimodal to unimodal patterns indicated environmental and dispersal filtering. Such bimodal occupancy-frequency patterns were validated in Longhursts classical biogeographical framework and in silico where observed bimodal patterns often aligned with specific biomes and provinces described by Longhurst and where found to be non-random in randomized datasets and mock communities. Taken together, our results show that application of metapopulation theory provides a framework for determining distinct microbial biomes maintained by environmental and dispersal filtering.

ecology↗

bioRxiv2017

There And Back Again -- Unraveling Mechanisms Of Bacterial Biogeography In The North Pacific Subtropical Gyre To And From Station ALOHA

Bacterially-mediated fluxes of energy and matter are dynamic in time and space coupled with shifts in bacterial community structure. Yet, our understanding of mechanisms shaping bacterial biogeography remains limited. Near-surface seawater was collected during transits between Honolulu and Station ALOHA in the North Pacific Subtropical Gyre to examine the shape of occupancy-frequency distributions (the different number of populations occupying different number of sites) and determine bacterial metapopulation dynamics. Bacterial 16S rRNA gene amplicons were sequenced from whole seawater and filter-size fractionated plankton DNA samples while also separating the community into distinct taxonomic groups at phyla/class and analyzing these compartments separately. For the total seawater (i.e. the >0.2 m size fraction) and picoplankton communities (i.e. the size fraction >0.2 m and < 3.0 m), but not the large size fraction community (i.e. the >3.0 m size fraction), most individual operational taxonomic units (OTUs) occupied a single site and the number of OTUs occupying different number of sites followed a significant bimodal pattern with several core OTUs occupying all sites. Nevertheless, only Cyanobacteria (in particular Prochlorococcus sp.) and in a few instances also Alphaproteobacteria (in particular SAR11 clade and Aegan-169 marine group bacteria) exhibited bimodal occupancy-frequency patterns. As expected, Prochlorococcus sp. had an inversed bimodal occupancy-frequency distribution with most OTUs found at all sites. Yet, there were individual satellite OTUs affiliated with Prochlorococcus sp. that were phylogenetically distinct from the core OTUs and only found at a single site. Collectively, these findings indicate that different compartments (size fractions and taxa) have different metapopulation dynamics. Bimodal patterns among the low diversity total and picoplankton communities but not in the high diversity large size fraction suggest that positive feedbacks between local abundance and occupancy are important when environmental conditions are homogenous and diversity is low.

ecology↗