Bacterial community shifts in organically perturbed sediments

Abstract

Bacterial abundance, diversity and sediment function were investigated in organically perturbed sediments under Tasmanian salmon (Salmo salar) farms and adjacent reference sites. Bacterial numbers increased as farming and organic loading progressed through the farm stocking cycle and declined during the fallow period, although not to prestocking levels. Bacterial numbers ranged between approximately 2 x 10(8) and 3 x 10(9) cells per gram of sediment and were higher at cage sites than reference sites. Microelectrode and respiration data also demonstrated a clear effect of organic loading on sediments. Denaturing gradient gel electrophoresis (DGGE) showed that bacterial communities shifted both in response to farm loading and its cessation. A seasonal effect on microbial communities was also evident. Although bacterial communities did shift again during the fallowing period, this shift was not necessarily a return to preloading communities. The complexity of community shifts may be affected by the vast functional redundancy of bacterial groups. All bacterial communities, including those at reference sites, were highly dynamic. Respiration studies of amended sediments indicated that fish farm sediments were at least as resilient and diverse as reference site communities. The results of this study indicate that the functional redundancy of highly complex bacterial communities contributes to their robustness. The relationship between diversity and stability in bacterial communities remains unclear and requires further investigation before an understanding of bacterial response to perturbation is possible.

Flavobacterial response to organic pollution

“…Although the primer set gives several mis-hits to phylotypes outside those targeted, it should be noted that all bands sequenced from DGGE gels fell within the target group, indicating that the primers employed did indeed target many of the dominant Flavobacteria in these sediments. Although our counts are subject to uncertainties at several stages of the QPCR process (DNA extraction, PCR, analysis) total bacterial counts are in good agreement to those we reported previously (Bissett et al 2007) as direct counts. Although the absolute numbers are slightly different, the same trends are clear, and at a minimum our QPCR represent good relative counts.…”

“…This was true for both absolute amounts of Flavobacteria and when their number was considered as a proportion of the total bacterial community, indicating that the increase in flavobacterial DNA was not simply a result of a general increase in all bacteria with farming. Bissett et al (2007) reported SYBR green direct bacterial counts for the same sediment samples. Their results showed the same trend as those revealed by our QPCR results for the total community.…”

“…For instance, the depth of the oxic zone decreased markedly (Bissett et al 2007) while sulphide concentration increased (Macleod et al 2004a) with organic loading. The increase in flavobacterial numbers during loading (also inferred by Bissett et al 2007) suggests that the Flavobacteria were able to adapt well to conditions under organic loading, further supporting the notion that these bacteria are important in organic matter remineralisation, even in anaerobic sediments. Although we have not directly assessed the role of the Flavobacteria in degradation or in stimulating benthic production, it is possible that they play an important role as initial biopolymer degraders in the investigated sediments.…”

“…That is, with organic loading, oxygen penetration decreased from ~4 to <1 mm and diffusive oxygen flux increased significantly (Bissett et al 2007). Sediment sulphide and ammonia concentrations also increased markedly (Macleod et al 2004b).…”

The impact of environmental perturbation on microbial community structure and dynamics: Factors affecting growth ofClonothrix fuscain groundwater

“…It is generally assumed that in these environments the diversity of microbial communities is massive (Torsvik et al 1996) and this diversity leads to a high degree of functional redundancy among microorganisms (Bissett et al 2007).…”