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Microbial biodiversity in Tasmanian caves

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Van de Kamp, Jodie Lee (2004) Microbial biodiversity in Tasmanian caves. PhD thesis, University of Tasmania.

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Abstract

Caves represent one of few remaining isolated planetary habitats, in terms of human
impact and characterisation of microbial biodiversity. Caves are unique environments
characterised by little or no light, low levels of organic nutrients, high mineral
concentrations and a stable microclimate providing ecological niches for highly specialised
organisms. Caves are not uniform environments in terms of geological and geochemical
characteristics, as they can vary from one to the other, eg. rock type, method of formation,
length, depth, number of openings to the surface, presence or absence of active streamways,
degree of impact by human visitation etc. Furthermore, on a smaller scale, various
microhabitats, with vast differences in community structure can exist within caves. Culture
studies point to the dominance of actinomycetes in caves and reveals great taxonomic
diversity within actinomycetes isolated. However it is widely accepted that only - 1 % of
microbes are cultured in the laboratory. Culture-independent methods are being
increasingly used to describe the composition of microbial communities and reveal
significantly broader diversity than culture-based studies. Nevertheless, to date our
knowledge of bacterial communities in caves is largely due to culture studies. Based on the
literature available, this study was initially aimed at examining culturable vs. non-culturable
diversity of actinomycetes in Entrance and Loons Caves and to gain an increased
understanding of the composition of cave microbial communities employing classical
isolation and advanced molecular detection methods.
As the study progressed the focus evolved as it became apparent that actinomycetes
dominated only very specific habitats, the dry sediment in Entrance Cave, and represented
only a minor fraction of the microbial biodiversity of most other microhabitats studied.
Entrance Cave dry sediments and inactive (dry) speleothems produced a higher number of
actinomycete isolates compared to saturated sediments and wet formations from Entrance
and Loons Caves. This was reinforced by the actinomycetes being the second most abundant
group (26.8%) detected in clone analysis of the dry Entrance sediment and low abundances
(4-16%) detected in saturated sediments from both Entrance and Loons Caves. Sediment
phylotypes and isolates identified in this study closely resemble species associated with
oligotrophic, chemolithotrophic and heterotrophic lifestyles indicating that these
communities survive by utilising a combination of metabolic pathways. Bacteria involved in
the nitrogen and sulfur cycles were important members of all sediment communities along
with hydrogen-oxidising bacteria. Pair-wise comparisons of sediment communities
demonstrated that they were more similar to each other within individual cave systems,
Entrance and Loons, rather than between microhabitat types (dry vs. wet sediment) though
saturated sediment from Entrance Cave did show a higher degree of similarity in
community composition to Loons Cave samples than the dry sediment from Entrance Cave. Saturated sediments were dominated by oligotrophs able to fix atmospheric gases,
methanotrophs and had a high proportion of rare phylotypes most likely representing new lineages related to microbes detected in anaerobic, anoxic environments, but low
abundances of heterotrophic microbes.
Geornicrobiological activities are no longer underestimated since studies have
shown that bacterial metabolism may lead to mineral precipitation or dissolution. Questions
remain as to the identity of these microbes and whether they are actively involved in
speleothem formation, or simply buried during mineral precipitation. Results demonstrated
a marked difference between sediment communities and those associated with calcite
speleothem and calcite mat samples. Results of ESEM and XRD analysis demonstrated that
calcite speleothem samples ME3 and MXl are true calcite moonrnilk (mondmilch).
Phylogenetic analyses and isolation results demonstrated the unique composition of the
microbial communities associated with moonrnilk deposits, predominantly composed of
nitrogen-fixing ~-Proteobacteria and psychrotrophic heterotrophic CFBs and to a lesser
extent, heterotrophic actinomycetes. Despite XRD and ESEM analysis showing similar calcite
composition and crystal morphology, phylogenetic results indicated that sample ME2
represented a very different rnicrohabitat to moonmilk samples, dominated by oligotrophic
a.-Proteobacteria and heterotrophic actinomycetes composing 84.2% of the total diversity.
Phylogenetic analyses and biodiversity indices reveal the striking similarities between
moonmilk samples from both Entrance and Exit Caves and the uniqueness of the calcite mat
in Entrance Cave. The one similarity in composition between all three calcite communities
was the presence of members of the Pseudonocardineae in particular of the genus
Saccharothrix, in all calcite samples.
165 rRNA gene sequencing of cave isolates detected high levels of diversity and
novelty, particularly of moonrnilk isolates. A total of two putatively novel genera (within the
CFBs and Actinobacteria) and 18 putatively novel species (of genera: Paracoccus,
Actinoplanes I Couchioplanes, Micromonospora, Amycolatopsis, Saccharothrix, Bacillus,
Paenibacillus, Methylobacterium, Porphyrobacter, Sphingomonas, Alcaligenes, Stenotrophomonas,
Xanthomonas) were identified.
This study represents the first reported culture-independent analysis of moonrnilk
microbial communities globally and of cave sediment communities in the Southern
Hemisphere. Information gained from this study and the discovery of actively growing
microbial communities appearing to precipitate CaC03 provides focus for important future
studies and represents a unique opportunity to examine the nature and extent of complex
microbe-mineral interactions in the formation of speleothems and implications for cave management. The biodiversity described acts as a baseline for assessing environmental
impacts and to identify factors influencing microbial biodiversity.

Item Type: Thesis (PhD)
Keywords: Actinomycetales, Microbial diversity, Microbial ecology, Cave ecology, Biospeleology
Copyright Holders: The Author
Copyright Information:

Copyright 2004 the Author - The University is continuing to endeavour to trace the copyright
owner(s) and in the meantime this item has been reproduced here in good faith. We
would be pleased to hear from the copyright owner(s).

Additional Information:

Thesis (Ph.D.)--University of Tasmania, 2005. Includes bibliographical references

Date Deposited: 04 Feb 2015 23:31
Last Modified: 11 Mar 2016 05:54
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