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

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

A single degenerated primer significantly improves COX1 barcoding performance in soil nematode community profiling

“…A proportion of the non-Nematoda ASVs were assigned to soil eukaryotes such as Arthropoda and Ascomycota. These organisms may represent a part of nematode gut microbiomes (McQueen et al, 2022) as soil nematodes feed on a large variety of food sources (Waeyenberge et al, 2019), alternatively their degraded debris can be carried by nematode cuticles (McQueen et al, 2023).…”

Population growth of two limno-terrestrial Antarctic microinvertebrates in different aqueous soil media

“…Knowledge of the fauna of Antarctic soil ecosystems has historically been limited with most studies assessing invertebrate presence and abundance under field conditions (Freckman et al 1997 ; Sinclair and Sjursen 2001 ; Adams et al 2014 ; Fontaneto et al 2015 ; Nielsen and King 2015 ; Baird et al 2019 ; Ball et al 2023 ). Recent advancements towards understanding their biology have been made with some taxa, including investigations of nematode life histories (De Tomasel et al 2013 ; Wharton and Raymond 2015 ), gut microbiomes (McQueen et al 2022 ; Parr McQueen et al 2023 ) and studies of microinvertebrate genetics (Thorne et al 2014 ; Xue et al 2024 ).…”

Bacterial communities associated with Acrobeles complexus nematodes recovered from tomato crops in South Africa

“…Microbiomes, including bacteria, fungi, viruses, and archaea, have been studied in a various range of animals, which play an important role in their development [ 7 ]. McQueen et al [ 8 ] studied internal and external microbiomes associated with Plectus murrayi , showing that Comamonadaceae, followed by Pseudomonaceae families, are the most dominant internal and external bacteria. The phylum Proteobacteria (46.45% of the bacterial taxa) was the most abundant bacterial phylum in Monhysteridae, Rhabditidae and Panagrolaimidae families of free-living bacterivores nematodes, followed by Bacteroidetes (20.47%), Actinobacteria (5.97%), Firmicutes (5.67%), and Cyanobacteria (2.47%) [ 9 ].…”