Global Trends in Marine Plankton Diversity across Kingdoms of Life

Cell, Год журнала: 2019, Номер 179(5), С. 1084 - 1097.e21

Опубликована: Ноя. 1, 2019

The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns diversity and underlying drivers remain poorly known, precluding projections responses global changes. Here we investigate latitudinal gradients predictors plankton across archaea, bacteria, eukaryotes, major virus clades using both molecular imaging data from Tara Oceans. We show a decline for most groups toward poles, mainly driven by decreasing temperatures. Projections into future suggest severe warming surface end 21st century could lead tropicalization in temperate polar regions. These changes may have multiple consequences ecosystem services are expected be particularly significant key areas carbon sequestration, fisheries, conservation. VIDEO ABSTRACT.

Язык: Английский

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AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential

Nucleic Acids Research, Год журнала: 2019, Номер 47(W1), С. W276 - W282

Опубликована: Апрель 11, 2019

Abstract Understanding the evolutionary background of a bacterial isolate has applications for wide range research. However generating an accurate species phylogeny remains challenging. Reliance on 16S rDNA identification currently popular. Unfortunately, this widespread method suffers from low resolution at level due to high sequence conservation. Currently, there is now wealth genomic data that can be used yield more designations via modern phylogenetic methods and multiple genetic loci. However, these often require extensive expertise time. The Automated Multi-Locus Species Tree (autoMLST) was thus developed provide rapid ‘one-click’ pipeline simplify workflow at: https://automlst.ziemertlab.com. This server utilizes Sequence Analysis (MLSA) produce high-resolution trees; does not preform multi-locus typing (MLST), related classification method. resulting tree also includes helpful annotations, such as clade secondary metabolite counts aid natural product prospecting. Distinct available web-interfaces, autoMLST automate selection reference genomes out-group organisms based one or query genomes. enables researchers perform rigorous analyses rapidly compared manual MLSA workflows.

Язык: Английский

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The Human Oral Microbiome in Health and Disease: From Sequences to Ecosystems

Microorganisms, Год журнала: 2020, Номер 8(2), С. 308 - 308

Опубликована: Фев. 23, 2020

The human oral cavity is home to an abundant and diverse microbial community (i.e., the microbiome), whose composition roles in health disease have been focus of intense research recent years. Thanks developments sequencing-based approaches, such as 16S ribosomal RNA metabarcoding, whole metagenome shotgun sequencing, or meta-transcriptomics, we now can efficiently explore diversity microbes, even if unculturable. Recent studies charted ecosystems how they change due lifestyle conditions. As progress, there increasing evidence important role microbiome conditions, which are not limited diseases cavity. This, turn, opens new avenues for microbiome-based diagnostics therapeutics that benefit from easy accessibility monitoring manipulation. Yet, many challenges remain ahead. In this review, survey main methodologies currently used highlight major findings enabled by these approaches. Finally, discuss future prospects field.

Язык: Английский

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Marine Plastic Debris: A New Surface for Microbial Colonization

Environmental Science & Technology, Год журнала: 2020, Номер 54(19), С. 11657 - 11672

Опубликована: Сен. 4, 2020

Plastics become rapidly colonized by microbes when released into marine environments. This microbial community—the Plastisphere—has recently sparked a multitude of scientific inquiries and generated breadth knowledge, which we bring together in this review. Besides providing better understanding community composition biofilm development ecosystems, critically discuss current research on plastic biodegradation the identification potentially pathogenic "hitchhikers" Plastisphere. The Plastisphere is at interface between its surrounding milieu, thus drives every interaction that synthetic material has with environment, from ecotoxicity new links food webs to fate plastics water column. We conclude so far not shown communities starkly differ other inert surfaces, particularly true for mature assemblages. Furthermore, despite progress been made field, recognize it time take plastic–Plastisphere–environment interactions step further identifying present gaps our knowledge offering perspective key aspects be addressed future studies: (I) physical characterization biofilms, (II) inclusion relevant controls, (III) study different successional stages, (IV) use environmentally concentrations biofouled microplastics, (V) prioritization gaining mechanistic functional communities.

Язык: Английский

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Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory

Clinical Microbiology Reviews, Год журнала: 2020, Номер 33(4)

Опубликована: Сен. 8, 2020

This review provides a state-of-the-art description of the performance Sanger cycle sequencing 16S rRNA gene for routine identification bacteria in clinical microbiology laboratory. A detailed technology and current methodology is outlined with major focus on proper data analyses interpretation sequences. The remainder article focused comprehensive evaluation application this method bacterial pathogens based multialignment In particular, existing limitations similarity within genus- species-level differentiation clinically relevant lack sequence currently available public databases highlighted. multiyear experience described large regional service direct broad-range PCR followed by detection appropriate samples. ability proteomics (matrix-assisted desorption ionization-time flight) versus genotyping compared. Finally, potential whole-genome analysis next-generation (NGS) to replace diagnostic use presented several applications, including barriers that must be overcome fully implement newer genomic methods microbiology. future challenge clinical, reference, research laboratories, as well industry, will translation vast amounts accrued NGS microbial into convenient algorithm testing schemes various applications (i.e., identification, genotyping, metagenomics microbiome analyses) so information can reported physicians format understood actionable. These challenges not faced microbiologists alone but every scientist involved domain where natural diversity genes sequences plays critical role disease, health, pathogenicity, epidemiology, other aspects life-forms. Overcoming these require global multidisciplinary efforts across fields do normally interact arena make interpretable actionable at bedside.

Язык: Английский

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Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses

Microbial Genomics, Год журнала: 2020, Номер 6(8)

Опубликована: Июль 24, 2020

Metagenomics and marker gene approaches, coupled with high-throughput sequencing technologies, have revolutionized the field of microbial ecology. is a culture-independent method that allows identification characterization organisms from all kinds samples. Whole-genome shotgun analyses total DNA chosen sample to determine presence micro-organisms domains life their genomic content. Importantly, whole-genome approach reveals diversity present, but can also give insights into functional potential identified. The based on specific region. It one describe composition taxonomic groups present in sample. frequently used analyse biodiversity ecosystems. Despite its importance, analysis metagenomic data quite challenge. Here we review primary workflows software for both approaches discuss current challenges field.

Язык: Английский

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Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities

The ISME Journal, Год журнала: 2021, Номер 15(7), С. 1956 - 1970

Опубликована: Фев. 21, 2021

Viruses are abundant yet understudied members of soil environments that influence terrestrial biogeochemical cycles. Here, we characterized the dsDNA viral diversity in biochar-amended agricultural soils at preplanting and harvesting stages a tomato growing season via paired total metagenomes size fraction (viromes). Size fractionation prior to DNA extraction reduced sources nonviral viromes, enabling recovery vaster richness populations (vOTUs), greater taxonomic diversity, broader range predicted hosts, better access rare virosphere, relative metagenomes, which tended recover only most persistent vOTUs. Of 2961 detected vOTUs, 2684 were recovered exclusively from while three alone. Both microbial communities differed significantly over time, suggesting coupled response rhizosphere recruitment processes and/or nitrogen amendments. Viral alone also structured along an 18 m spatial gradient. Overall, our results highlight utility viromics reveal similarities between community dynamics throughout suggest partial decoupling driving their distributions, potentially due differences dispersal, decay rates, sensitivities heterogeneity.

Язык: Английский

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Marine biofilms constitute a bank of hidden microbial diversity and functional potential

Nature Communications, Год журнала: 2019, Номер 10(1)

Опубликована: Янв. 31, 2019

Abstract Recent big data analyses have illuminated marine microbial diversity from a global perspective, focusing on planktonic microorganisms. Here, we analyze 2.5 terabases of newly sequenced datasets and the Tara Oceans metagenomes to study biofilm-forming We identify more than 7,300 ‘species’ that are undetected in seawater analyses, increasing known oceans by 20%, provide evidence for differentiation across oceanic niches. Generation gene distribution profile reveals functional core biofilms, comprised genes variety phyla may play roles stress responses microbe-microbe interactions. Analysis 479 genomes reconstructed biofilm novel biosynthetic clusters CRISPR-Cas systems. Our highlight previously underestimated ocean diversity, allow mining lineages resources.

Язык: Английский

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Identifying biases and their potential solutions in human microbiome studies

Microbiome, Год журнала: 2021, Номер 9(1)

Опубликована: Май 18, 2021

Abstract Advances in DNA sequencing technology have vastly improved the ability of researchers to explore microbial inhabitants human body. Unfortunately, while these studies uncovered importance communities our health, they often do not result similar findings. One possible reason for disagreement results is due multitude systemic biases that are introduced during sequence-based microbiome studies. These begin with sample collection and continue be throughout entire experiment leading an observed community significantly altered from true underlying composition. In this review, we will highlight various steps typical where significant bias can introduced, review current efforts within field aim reduce impact biases.

Язык: Английский

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Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies

Microbiome, Год журнала: 2022, Номер 10(1)

Опубликована: Июль 8, 2022

Abstract Background The 16S rRNA gene is used extensively in bacterial phylogenetics, species delineation, and now widely microbiome studies. However, the suffers from intragenomic heterogeneity, reports of recombination an unreliable phylogenetic signal are accumulating. Here, we compare core phylogenies to constructed using concatenations estimate strength for gene, its hypervariable regions, all genes at intra- inter-genus levels. Specifically, perform four intra-genus analyses ( Clostridium , n = 65; Legionella 47; Staphylococcus 36; Campylobacter 17) one analysis [41 genera human gut (31 families, 17 orders, 12 classes), 82]. Results At both taxonomic levels, was recombinant subject horizontal transfer. level, showed lowest levels concordance with genome phylogeny (50.7% average). Concordance regions lower still, entropy masking providing little no benefit. A major factor influencing SNP count, which a positive logarithmic association. Using this relationship, determined that 690 ± 110 SNPs were required 80% (average count 254). We also found wide range 16S-23S-5S operon copy number among genomes (1–27). whole markedly higher (73.8% — 10th out 49 loci); however, most concordant (V4, V3-V4, V1-V2) ranked third quartile (62.5 60.0%). Conclusions Ramifications poor performance far reaching. For example, addition incorrect species/strain delineation inference, it has potential confound community diversity metrics if information incorporated popular approaches such as Faith’s UniFrac. Our results highlight problematic nature these their use (along masking) discouraged. Lastly, strong metrics.

Язык: Английский

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