Chemotaxis shapes the microscale organization of the ocean’s microbiome

Lambert, Bennett S.; Parks, Donovan H.; Siboni, Nachshon; Bramucci, Anna R.; Ostrowski, Martin; Signal, Bethany; Lutz, Adrian; Mendis, Himasha; Rubino, Francesco; Fernández, Vicente; Stocker, Roman; Hugenholtz, Philip; Tyson, Gene W.; Seymour, Justin R.

doi:10.1038/s41586-022-04614-3

Cited by 84 publications

(67 citation statements)

References 69 publications

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“…Given the many thousands of individual microbial species and metabolites present in seawater communities, it has been challenging to connect specific metabolic processes to the microbial taxa responsible (Cavaco et al, 2022;Paoli et al, 2022). Advances in molecular and chemical tools have improved resolution and identification of microbially cycled metabolites in seawater communities (Moran et al, 2016;Durham, 2021;Vallet et al, 2021;Raina et al, 2022). Genome-based studies of marine microbial plankton have been useful in reconstructing potential metabolisms, ecological functions, and evolutionary relationships of taxonomic groups.…”

Section: Introductionmentioning

confidence: 99%

Chemotaxonomic patterns in intracellular metabolites of marine microbial plankton

et al. 2022

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Most biological diversity on Earth is contained within microbial communities. In the ocean, these communities dominate processes related to carbon fixation and nutrient recycling. Yet, specific factors that determine community composition and metabolic activity are difficult to resolve in complex microbial populations, complicating predictions of microbial processes in a changing ocean. Microbial metabolism generates small organic molecules that reflect both the biochemical and physiological diversity as well as the taxonomic specificity of these biological processes. These small molecules serve as the conduit for taxon-specific signaling and exchange. Here, we use liquid chromatography-mass spectrometry (LC-MS)-based metabolomics to taxonomically categorize 111 metabolites that include small molecules in central and secondary metabolism across 42 taxa representing numerically dominant and metabolically important lineages of microbial autotrophs and heterotrophs. Patterns in metabolite presence-absence broadly reflected taxonomic lineages. A subset of metabolites that includes osmolytes, sulfurcontaining metabolites, sugars, and amino acid derivatives provided chemotaxonomic information among phytoplankton taxa. A variety of phytohormones and signaling molecules were predominantly found in the heterotrophic bacteria and archaea, expanding knowledge of metabolites implicated in modulating interactions between microbes. This chemotaxonomic inventory of marine microbial metabolites is a key step in deciphering metabolic networks that influence ocean biogeochemical cycles.

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Section: Introductionmentioning

confidence: 99%

Chemotaxonomic patterns in intracellular metabolites of marine microbial plankton

et al. 2022

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“…In contrast, it was reported that phage infection could stop the host macromolecular synthesis promptly and completely (75). Pioneering work on bacterial motility revealed that phages could exert multiple roles in the hosts, including contributing to searching more adaptive environments, serving as virulence factors for pathogens and being conducive to symbiotic relationships (76–79). The downregulation of host genes related to material catabolic processes and bacterial motility-related pathways was consistent with other temperate phage infections (18, 23, 80, 81).…”

Section: Discussionmentioning

confidence: 99%

A novel inovirus reprograms metabolism and motility of marine Alteromonas

Peng

Chen

Jian

et al. 2022

Preprint

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Members from the Inoviridae family with striking features are widespread, highly diverse and ecologically pervasive across multiple hosts and environments; however, very small amount of inoviruses have been isolated and studied. Here, a filamentous phage infecting Alteromonas abrolhosensis, designated ΦAFP1, was isolated from the South China Sea and represented as a novel genus of Inoviridae. ΦAFP1 consisted of a single-stranded DNA genome (5986 bp), encoding eight putative ORFs. Comparative analyses revealed ΦAFP1 could be regarded as genetic mosaics, which especially came from Ralstonia and Stenotrophomonas phages. The temporal transcriptome analysis of A. abrolhosensis to ΦAFP1 infectionreveals that 7.78% of the host genes were differentially expressed. The genes involved in translation processes, ribosome pathways and degradation of multiple amino acid pathways at plateau period were upregulated, while host material catabolic and bacterial motility-related genes were downregulated, indicating that ΦAFP1 might hijack the energy of the host for the synthesis of phage proteins. ΦAFP1 exerted the step-by-step control on host genes through the appropriate level of the utilizing host resources, affirming a new non-standard regulatory strategy of viral temperately control over the host transcriptional profile. Our study provides novel information for a better understanding of filamentous phage characteristics and phage-host interactions.

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“…The sensory machinery is energetically costly [9,29], but helps individuals reach reproductively favorable habitats [47], including motile hosts that emit chemical signals [48]. For example, marine bacteria and archaea exhibit strong chemotaxis towards phytoplankton-produced organic matter, helping them find resource hotspots in the open ocean [49].…”

Section: Navigation Capacities -Taxismentioning

confidence: 99%

Scaling up and down: movement ecology for microorganisms

Wisnoski¹,

Lennon²

2022

Preprint

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Movement is critical for the fitness of organisms, both large and small. It dictates how individuals acquire resources, evade predators, exchange genetic material, and respond to stressful environments. Movement also influences ecological and evolutionary dynamics at scales beyond the individual organism. However, the links between individual motility and the processes that generate and maintain microbial diversity are poorly understood. Movement ecology is a framework linking the physiological and behavioral properties of individuals to movement patterns across scales of space, time, and biological organization. By synthesizing insights from cell biology, ecology, and evolution, we expand theory from movement ecology to predict the causes and consequences of microbial movements from small to large scales.

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Chemotaxis shapes the microscale organization of the ocean’s microbiome

Cited by 84 publications

References 69 publications

Chemotaxonomic patterns in intracellular metabolites of marine microbial plankton

Chemotaxonomic patterns in intracellular metabolites of marine microbial plankton

A novel inovirus reprograms metabolism and motility of marine Alteromonas

Scaling up and down: movement ecology for microorganisms

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