Abstract
BackgroundThe koala (Phascolarctos cinereus), an iconic yet endangered specialised folivore experiencing widespread decline across Australia, is the focus of many conservation programs. Whilst animal translocation and progressive conservation strategies such as faecal inoculations may be required to bring this species back from the brink of extinction, insight into the variation of host-associated gut microbiota and the factors that shape this variation are fundamental for their success. Despite this, very little is known about the landscape variability and factors affecting koala gut microbial community dynamics. We used large scale field surveys to evaluate the variation and diversity of koala gut microbiotas and compared these diversity patterns to those detected using a population genetics approach. Scat samples were collected from five locations across South East Queensland with microbiota analysed using 16S rRNA gene amplicon sequencing.ResultsAcross the landscape koala gut microbial profiles showed large variability, with location having a large effect on bacterial community composition and bacterial diversity. Certain bacteria were found to be significantly differentially abundant amongst locations; koalas from Noosa showed a depletion in two bacterial orders (Gastranaerophilales and Bacteroidales) which have been shown to provide beneficial properties to their host. Koala gut microbial patterns were also not found to mirror population genetic patterns, a molecular tool often used to design conservation initiatives.ConclusionsOur data shows that koala gut microbiotas are extremely variable across the landscape, displaying complex micro- and macro- spatial variation. By detecting locations which lack certain bacteria we identified koala populations that may be under threat from future microbial imbalance or dysbiosis. Additionally, the mismatching of gut microbiota and host population genetic patterns exposed important population structure that has previously gone undetected across South East Queensland. Overall, this baseline data highlights the importance of integrating microbiota research into conservation biology in order to guide successful conservation programs such as species translocation and the implementation of faecal inoculations.
Highlights
The koala (Phascolarctos cinereus), an iconic yet endangered specialised folivore experiencing wide‐ spread decline across Australia, is the focus of many conservation programs
Location boundaries were defined by local council borders (Fig. 1), and whilst we acknowledge that koalas do not recognise these anthropomorphised borders and may pass between them, koala conservation is often conducted at the local council level, for this research to be valuable to council conservation strategies, we maintained these council management units within our analyses
11 phyla were identified across samples (Fig. 2), and in accordance with previous studies [28,29,30, 43], the gut microbiota of koalas across South East Queensland (SEQ) was dominated by the bacterial phyla Firmicutes, Bacteroidetes (19.18% ± 14.74%) and Proteobacteria (12.51% ± 25.95%; Fig. 2, Additional file 2: S3)
Summary
The koala (Phascolarctos cinereus), an iconic yet endangered specialised folivore experiencing wide‐ spread decline across Australia, is the focus of many conservation programs. Whilst animal translocation and progres‐ sive conservation strategies such as faecal inoculations may be required to bring this species back from the brink of extinction, insight into the variation of host-associated gut microbiota and the factors that shape this variation are fundamental for their success. Despite the growing evidence over the last century describing the influence gut microorganisms have on vertebrate species [5], the field of conservation biology has largely concentrated on the macroecological, rather than the microbial world [6,7,8]. Gut microbial studies can identify microorganisms important for animal health, survival, and fitness [16], but can help shape conservation initiatives where animals may be faced with a sudden change in environmental conditions and/or diet, such as animal translocation [17] or reintroduction programmes [7, 18]. Baseline knowledge of host-microbial interactions provides an important first step in determining whether specific gut microbes (or microbial genes) are required to prime the host’s immune system in order to aid resistance to future environmental perturbations and/or pathogens
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