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Microbial ecology of aquaculture sediments

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Bissett, Andrew (2004) Microbial ecology of aquaculture sediments. PhD thesis, University of Tasmania.

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Abstract

Sediment bacterial communities were studied at two Tasmanian salmon farm sites and
adjacent unimpacted reference sites. Microbial biomass and total diversity were
investigated as well the diversity and population density of the Cytophaga-Flavobacteria-Bacteroides
group (CFB) and beta-proteobacterial ammonia oxidizers
(AOB). The study aimed to develop a conceptual understanding of microbial
community dynamics in response to disturbance and to assess the efficacy of farm
fallowing practices in allowing sediment bacterial communities to recover from
organic loading.
Sediments from two salmon farms were studied over two full farm production cycles
of 12 months each. Each cycle consisted of a nine-month stocking period, during
which organic loading occurred, followed by a three month fallow period, during
which no loading occurred. To represent the range of sediment conditions prevalent
at Tasmanian salmon farms, farms with differing sediment conditions were chosen.
Sediment at farm 1 was coarse grained, while at that at farm 2, sediment was fine
grained. Sampling was conducted at the beginning of each cycle and at the end of
each period within a cycle.
Bacterial numbers increased as farming and organic loading progressed through the
farm cycle and declined during the fallowing period, although not to pre-stocking
levels. Bacterial numbers ranged between approximately 2 x 108 and 3 x 109 cells/g
sediment and were generally higher at cage sites than reference sites. Six, 16S rRNA gene clone libraries were constructed, comprising more than 600
clones sequences, from both cage and reference sites. These revealed that both cage
and reference site sediments at both farms showed a very high level of diversity.
Reference sites were dominated by delta and gamma-proteobacteria and CFB group
bacteria. Cage site sediments also showed large numbers of these phylotypes, as well
as members of the alpha and epsilon-proteobacteria. Diversity and coverage indices
indicated that the diversity of all sediments studied was much greater than that
detected in this study, despite a large sampling effort. All clone libraries were shown
to be statistically different from one another, further supporting the idea that coverage was low. Many phylotypes did not group with cultured bacteria, but grouped with
other environmental clones from a wide array of marine benthic environments. Clone
libraries indicated the presence of a large number of bacterial types, including the
Myxobacteria. Although thought to be unable to grow under marine conditions, the
large number of Myxobacteria clones found in this study further supports the idea that
this may not be the case.
Denaturing gradient gel electrophoresis (DGGE) showed that bacterial communities
shifted both in response to farm loading and the cessation of this loading.
Communities also shifted frequently at reference site communities, indicating the
highly dynamic nature of sediment bacterial communities and the possibility of a
seasonal effect. Although bacterial communities did shift again during the fallowing
period this shift was not necessarily evidence of a return to pre-loading communities.
The complexity of community shifts and their interpretation could be attributed to the
vast functional redundancy of bacterial groups. Respiration studies indicated that
cage site sediments were as resilient and as diverse as reference site sediments. CFB and AOB communities too showed shifts and counter shifts with organic loading
and fallowing. Again the exact nature of the shifts was difficult to elucidate:
communities did not show a simple shift/counter-shift response to farm loading and
fallowing. Real-time PCR showed that CFB numbers increased with farming and
decreased with fallowing. The response of the CFB group to organic loading was
typical of that expected of an opportunistic group. Real-time PCR analysis of the
AOB showed that farm loading had little effect on their numbers. The AOB were
absent from clone libraries, but analysis of DGGE band sequences showed that a
diverse AOB community was present at both farms at all times during the study, thus
maintaining at least the potential for the coupled nitrification/denitrification process.
Bacterial community shifts and response to perturbation are difficult to interpret, as a
result of the massive functional redundancy exhibited by bacteria. The sediment
bacterial community though, appeared to be determined by sediment environmental
parameters. This is in contrast to sediment infaunal communities, which tend to
respond according to the equilibrium theory. Bacterial biomass and diversity responded to farm fallowing practices, thus these practices appeared efficacious in
maintaining diverse, resilient sediment bacterial communities.

Item Type: Thesis (PhD)
Keywords: Marine sediments, Aquatic ecology, Water, Fish culture
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 (PhD.)--University of Tasmania, 200. Includes bibliographical references

Date Deposited: 25 Nov 2014 00:54
Last Modified: 11 Mar 2016 05:54
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