External and internal microbiomes of Antarctic nematodes are distinct, but more similar to each other than the surrounding environment

Journal of Nematology, Journal Year: 2023, Volume and Issue: 55(1)

Published: Feb. 1, 2023

Abstract Host-associated microbiomes have primarily been examined in the context of their internal microbial communities, but many animal species also contain microorganisms on external host surfaces that are important to physiology. For nematodes, single strains bacteria known adhere cuticle (e.g., Pasteuria penetrans ), structure a full community is uncertain. In prior research, we showed gut nematodes ( Plectus murrayi , Eudorylaimus antarcticus ) and tardigrades from Antarctica’s McMurdo Dry Valleys were distinct surrounding environment driven by identity. Building this work, extracted an additional set individuals containing intact amplified them for 16S 18S rRNA metabarcoding. Our results bacterial more diverse than microbiomes, less environment. Host-specific compositional patterns observed, most similar respective microbiomes. However, influenced were. Non-host eukaryotic communities diversity exhibited stochastic assembly compared suggesting lack structured microbiome. Altogether, provide evidence nematode tardigrade cuticles inhabited robust substantially host, albeit so are.

Language: Английский

---

Different trematode parasites in the same snail host: Species‐specific or shared microbiota?

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(19), P. 5414 - 5428

Published: Aug. 24, 2023

The concept that microbes associated with macroorganisms evolve as a unit has swept evolutionary ecology. However, this idea is controversial due to factors such imperfect vertical transmission of microbial lineages and high microbiome variability among conspecific individuals the same population. Here, we tested several predictions regarding microbiota four trematodes (Galactosomum otepotiense, Philophthalmus attenuatus, Acanthoparyphium sp. Maritrema novaezealandense) parasitize snail host We predicted each parasite species would harbour distinct microbiota, composition similarity decreasing increasing phylogenetic distance species. also trematode co-infecting individual influence other's microbiota. detected significant differences in alpha beta diversity, well differential abundance, found no evidence phylogenetically closely related had more similar uncovered indicator bacterial taxa were significantly Trematode sharing showed mostly one-sided exchanges, community one approaching other. hypothesize natural selection acting on specific may be important maintain horizontally acquired microbes, playing role. In particular, consistent diverse bacteriota than others, potentially result stronger stabilizing pressures. conclude species-specific processes shape assembly different exploiting

Language: Английский

---

Pinpointing the microbiota of tardigrades: what is really there?

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 24, 2024

Abstract Microbiota have been proposed as an important aspect of tardigrade biology, but little is known about their diversity and distribution. Here, we attempted to characterize the microbiota 44 cultured species tardigrades using 16S rRNA amplicon sequencing, different specimen pooling strategies, various DNA extraction kits, multiple types controls. We also estimated number microbes in samples synthetic spike-ins. Additionally, reanalyzed data from previous studies. Our results suggest that microbial community profiles are dominated by bacterial OTUs genotypes originating food, medium, or laboratory reagents. found strains consistently enriched certain (relative culture media controls), which indicates likely symbiotic associations, reads representing putative true tardigrade-associated rarely exceeded 20% datasets. Some identified matched symbionts other However, serious contamination issues with studies microbiome, making some conclusions questionable. conclude not universally dependent on specialized highlight necessary safeguards future microscopic organisms.

Language: Английский

---

Probing the functional significance of wild animal microbiomes using omics data

Published: Feb. 13, 2024

Host-associated microbiomes are thought to play a key role in host physiology and fitness, but this conclusion mainly derives from studies of handful animal models humans. To test the generality conclusion, non-model wild animals needed. However, whilst microbiome taxonomic diversity has recently received much attention, characterization its functional potential is lagging behind. Functional “omics” approaches, such as metagenomics, metatranscriptomics, metabolomics, represent promising techniques probe significance host-associated wild. In review, we propose (1) briefly define main available omics tools along with their strengths limitations, (2) summarise advances enabled by understand function human models, (3) showcase examples how these methods have already brought invaluable insights into (4) provide guidelines on implement address outstanding questions field microbiomes. conclude, suggest that approach once presence an abundant resident microbiota been established using more traditional (and less expensive) approaches qPCR metabarcoding.

Language: Английский

---

Comparative analysis of gut microbiome of mangrove brachyuran crabs revealed patterns of phylosymbiosis and codiversification

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(12)

Published: May 7, 2024

The acquisition of microbial symbionts enables animals to rapidly adapt and exploit novel ecological niches, thus significantly enhancing the evolutionary fitness success their hosts. However, dynamics host-microbe interactions implications remain largely underexplored in marine invertebrates. Crabs family Sesarmidae (Crustacea: Brachyura) are dominant inhabitants mangrove forests considered keystone species there. Their rapid diversification, particularly after adopting a plant-feeding lifestyle, is believed have been facilitated by symbiotic gut microbes, enabling successful colonization intertidal terrestrial environments. To investigate patterns mechanisms shaping communities role microbes evolution Sesarmidae, we characterized compared microbiome compositions across 43 crab from other mangrove-associated families using 16S metabarcoding. We found that assemblages crabs primarily determined host identity, with secondary influence environmental factors such as microhabitat sampling location, lesser extent influenced biological sex region. While phylosymbiosis (i.e. when community relationships recapitulate phylogeny hosts) were consistently observed all beta-diversity metrics analysed, strength varied families. This suggests bacterial each differentially shaped different degrees filtering and/or processes. Notably, displayed signals cophylogeny its core genera, which likely play crucial functional roles hosts providing lignocellulolytic enzymes, essential amino acids, fatty acids supplementation. Our results support hypothesis contribution herbivory terrestrialization crabs, highlighting tight association codiversification holobiont.

Language: Английский

---

Exploring the landscape of symbiotic diversity and distribution in unicellular ciliated protists

Microbiome, Journal Year: 2024, Volume and Issue: 12(1)

Published: May 24, 2024

The eukaryotic-bacterial symbiotic system plays an important role in various physiological, developmental, and evolutionary processes. However, our current understanding is largely limited to multicellular eukaryotes without adequate consideration of diverse unicellular protists, including ciliates.

Language: Английский

---

Soil properties predict below‐ground community structure, but not nematode microbiome patterns in semi‐arid habitats

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(18)

Published: Aug. 22, 2024

Abstract Microbial and microeukaryotic communities are extremely abundant diverse in soil habitats where they play critical roles ecosystem functioning services that essential to health. Soil biodiversity is influenced by above‐ground (vegetation) below‐ground factors (soil properties), which together create habitat‐specific conditions. However, the compound effects of vegetation properties on less studied or often focused one component biota. Here, we integrate metabarcoding (16S 18S rRNA genes) nematode morphology assess habitat shaping microbial as well nematode‐associated microbiomes. We show both bulk density) were major structuring semi‐arid habitats. Despite having lower nutrients pH, denser soils displayed significantly higher alpha diversity than dense across datasets. Nematode‐associated microbiomes have diversity, strongly differ from microbes more likely respond microscale variations among samples density. Consequently, different lineages trophic groups display similar associated when sharing same microhabitat. Different microbiome taxa enriched within specific (e.g. Mycobacterium , Candidatus Cardinium ) highlighting potentially new species‐specific associations may confer benefits their hosts. Our findings highlight importance exploring above‐ community structure terrestrial habitats, how fine‐scale analyses for understanding patterns host‐associated

Language: Английский

---

The draft genome of the microscopic Nemertoderma westbladi sheds light on the evolution of Acoelomorpha genomes

Frontiers in Genetics, Journal Year: 2023, Volume and Issue: 14

Published: Sept. 26, 2023

Xenacoelomorpha is a marine clade of microscopic worms that an important model system for understanding the evolution key bilaterian novelties, such as excretory system. Nevertheless, genomics has been restricted to few species either can be cultured in lab or are centimetres long. Thus far, no genomes available Nemertodermatida, one group's main clades and whose origin dated more than 400 million years ago.

Language: Английский

---

Water temperature and disease alters bacterial diversity and cultivability from American lobster (Homarus americanus) shells

iScience, Journal Year: 2023, Volume and Issue: 26(5), P. 106606 - 106606

Published: April 8, 2023

The American lobster, Homarus americanus, is an economically valuable and ecologically important crustacean along the North Atlantic coast of America. Populations in southern locations have declined recent decades due to increasing ocean temperatures disease, these circumstances are progressing northward. We monitored 57 adult female lobsters, healthy shell diseased, under three seasonal temperature cycles for a year, track bacterial communities using culturing 16S rRNA gene sequencing, progression epizootic disease visual assessment, antimicrobial activity hemolymph. richness taxa present, evenness abundance, community similarity between lobsters was affected by water at time sampling, over based on regimes, severity, molt stage. Several bacteria were prevalent lobster shells but missing or less abundant diseased shells, although some found all regardless health status.

Language: Английский

---

Natural populations of the putative ancient asexual Darwinula stevensoni (Crustacea, Ostracoda) differ in their microbiomes

Hydrobiologia, Journal Year: 2023, Volume and Issue: 850(17), P. 3719 - 3741

Published: June 7, 2023

Language: Английский

---