Microbial Physiology And Metabolism Daniel Caldwell PdfBy Battmigfena In and pdf 18.04.2021 at 02:27 4 min read
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- [PDF.47wb] Microbial Physiology and Metabolism
- Bacterial Physiology and Metabolism
- Microbial Physiology & Metabolism
They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes , ranging from spheres to rods and spirals.
[PDF.47wb] Microbial Physiology and Metabolism
The sea cucumber Holothuria scabra was cultured on sediments under contrasting redox regimes; fully oxygenated oxic and redox stratified oxic-anoxic.
Taxonomically, metabolically and functionally distinct bacterial communities developed between the redox treatments with the oxic treatment supporting the greater diversity; redox regime and dissolved oxygen levels were the main environmental drivers. Oxic sediments were colonised by nitrifying bacteria with the potential to remediate nitrogenous wastes. Percolation of oxygenated water prevented the proliferation of anaerobic sulphate-reducing bacteria, which were prevalent in the oxic-anoxic sediments.
At the predictive functional level, bacteria within the oxic treatment were enriched with genes associated with xenobiotics metabolism. Oxic sediments showed the greater bioremediation potential; however, the oxic-anoxic sediments supported a greater sea cucumber biomass. Overall, the results indicate that bacterial communities present in fully oxic sediments may enhance the metabolic capacity and bioremediation potential of deposit-feeder microbial systems.
This study highlights the benefits of incorporating deposit-feeding invertebrates into effluent treatment systems, particularly when the sediment is oxygenated. Bacterial communities present in marine sediments play significant ecological and biogeochemical roles in organic matter decomposition and nutrient cycling. Abiotic and biotic factors including the chemical environment of sediments e.
Deposit-feeding macrofauna further affect sediment microbiology through burying activities bioturbation that reworks the sediment and enhances sediment-water exchange, stimulating bacterial production and net mineralization rates 3. Tight coupling therefore exists between bioturbation, redox conditions, microbial communities, and detritus processing 4.
To date, a lack of understanding of the complex interactions between bacteria and deposit-feeders has created a knowledge gap in microbial mineralization within aquaculture systems. Information on this relationship offers huge potential to optimise future designs for sustainable aquaculture production technologies. This can produce water column hypoxia and the release of toxic metabolites e. Deposit-feeding sea cucumbers are the focus of growing attention as potential bioremediators in aquaculture systems due to their ability to convert faeces and waste feed into high value secondary biomass 6 , 7 , 8.
In situ bioremediation technologies frequently employ the addition of external electron acceptors, most frequently oxygen, to enhance the aerobic decomposition of organic matter and alleviate the constraints imposed by the naturally slow mineralization process in sediments 9. The percolation of oxygenated water, one of the most cost-effective approaches currently used for in situ sediment remediation, is applicable to the development of aquaculture bioremediation systems that integrate epibenthic deposit-feeders.
Combining bioremediation technologies increasing oxidant supply with the production of high value secondary livestock e. Robinson et al. Sea cucumbers reared on fully oxic sediments experienced stunted growth and yielded a lower biomass relative to those reared on oxic-anoxic sediments which mirror the natural habitat of H. The active circulation of oxygenated water successfully maintained sediment under fully oxic conditions and appeared to increase the rate of organic matter degradation.
We hypothesised that the carbon oxidation and nitrogen cycling conditions within the contrasting redox regimes affected both the quality and quantity of food resources available for deposit-feeder growth. We further hypothesised that the oxic-anoxic sediments would harbour microbial communities that were dominated by heterotrophic bacteria operating anaerobic and fermentative metabolisms.
In theory, this should provide a steady release of more nutritionally favourable food resources for deposit-feeders than fully aerobic systems.
A number of studies have used next-generation sequencing to investigate bacterial community composition in the sediments of sea cucumber aquaculture ponds and adjacent natural habitats 11 , 12 ; however, to date, no study has investigated the effect of oxygen supply on sediment microbial composition and community structure in aquaculture systems with a view to improving their bioremediation capacities.
An exploration of the mechanisms by which bacterial community composition is affected by abiotic and biotic factors could contribute to improving our understanding of aquaculture effluent treatment systems. Currently, the relationships between bacterial community structure and the redox regime of marine sediments are poorly understood Therefore, it is important to investigate the effect of oxygen availability on the structure and functional potential of bacterial communities in sediment-based bioremediation systems This is a timely study due to the high level of interest from governments worldwide to increase aquaculture production to address global food security issues, including the provision of cost-effective and sustainable aquaculture waste treatment solutions.
This study presents novel findings that advance observations detailed in Robinson et al. The environmental drivers behind changes in the microbial communities are evaluated and discussed in relation to the use of deposit-feeders for bioremediation purposes. The water temperature in the oxic-anoxic treatment Also, the oxic treatment produced more than double the cyanobacterial biomass Growth rates in both treatments were positive throughout the duration of the trial, however the rate decreased over time.
The biomass density increased linearly in both treatments up to Day 56; however, it began to decrease in the oxic treatment during the final third of the trial. Sea cucumbers in the oxic-anoxic treatment achieved a final mean density of Subsequent to quality control, primer trimming, size exclusion, and removal of unassigned bacteria and archaea, a total of 47, optimised reads from the 15 samples remained. Sequences were subsampled to 1, the minimum number of sequences in all samples.
Rarefaction curves indicated that the oxic treatment was not sampled to saturation whereas sequencing depth was sufficient for the oxic-anoxic treatment Supplementary Fig. The richness estimators and diversity indices were all significantly higher in the oxic treatment Table 2 indicating that the sediments maintained under a fully oxic redox regime harboured more diverse and stable bacterial communities than the stratified oxic-anoxic sediments.
There were 20 unique phyla, 21 candidate divisions, and two phyla proposed by the Greengenes database [Caldithrix] and [Thermi]. Bacteroidetes had the highest sequence abundance representing Unclassified bacteria 2. Similarly, phylogenetic groups from the phyla Thermotogae, Fibrobacteres, [Thermi] and the candidate divisions KSB3 and LCP were only present in the oxic-anoxic sediments.
The relative abundance of the bacterial reads classified at phylum level including Proteobacteria sub-classes from the different sediment redox regimes and depths. The sediment redox regime led to significant differences in the relative abundance of eight phyla, five candidate divisions and four of the Proteobacteria classes. Figure 3 presents a taxonomic representation of the statistically significant relevant biomarkers that were identified in the oxic-anoxic red and oxic green treatments.
Beta diversity analysis performed at the phylum level revealed that the bacterial communities were distinct between the oxic and oxic-anoxic treatments. The samples clustered into two clear groups by treatment along axis 1 that explained Sediment redox potential was the only significant environmental variable driving differences in bacterial community structure between treatments Supplementary Table 1.
The phylogenetic distribution of microbial lineages associated with the two different sediment redox regimes oxic-anoxic and oxic. Lineages with linear discriminant analysis LDA values of 5. The six rings of the cladogram stand for domain innermost , phylum, class, order, family and genus. Light green circles are biomarkers with LDA scores of less than 5. Labels are shown at the phylum level only. Bacterial phyla with significantly different relative abundances between the oxic-anoxic and oxic redox regimes Kruskal-Wallis test.
A principal components analysis biplot of the correlation between the bacterial community composition and the environmental parameters plotted as vectors. The only taxa containing biomarkers specific to both treatments were the phyla Chloroflexi, Plantomycetes, and the class Deltaproteobacteria.
Fifty were identified as consistently statistically different in the oxic treatment compared with 36 in the oxic-anoxic treatment.
The biomarkers enriched in the oxic treatment were classified within the phyla Actinobacteria, Bacteroidetes, Caldithrix, Chloroflexi, Cyanobacteria, Nitrospirae, Planctomycetes, Verrucomicrobia; the classes Alpha- Delta- and Gammaproteobacteria and the candidate division TM6. The oxic-anoxic treatment had 16 biomarkers classified within eight phyla, including; Bacteroidetes, Chlorobi, Chloroflexi, Firmicutes, Fusobacteria, Planctomycetes, Spirochaetes, Tenericutes, the subclasses Delta-, and Epsilonproteobacteria and the three candidate divisions H, KSB3, and OP8 Fig.
Classification of the bacterial biomarkers according to their oxygen-related physiology highlighted clear differences between treatments Fig. The majority of biomarkers in the oxic-anoxic treatment were strict or obligate anaerobes, whereas all of the biomarkers in the fully oxic sediments were obligate or facultative aerobes. Similarly, classification based on the type of dissimilatory metabolism revealed clear differences in the metabolic capacity and putative functional roles between treatments.
Biomarkers significantly enriched in the oxic treatment covered a broad spectrum of dissimilatory metabolisms including heterotrophs, taxa with aerobic and anaerobic respiratory and fermentative metabolisms; chemolithotrophs; methylotrophs and phototrophs performing both oxygenic and anoxygenic photosynthesis Supplementary Table 2.
In contrast, all biomarkers enriched in the oxic-anoxic treatment were heterotrophs Supplementary Table 3. The lower degree of accuracy for the oxic sediments may be due to higher bacterial diversity and increased abundance of bacteria that do not yet have sequenced representatives. A total of pathways were indicated at the three-tier level of functional categories defined by the BRITE hierarchy. There were significant differences between treatments in the predicted bacterial metagenome at the two-tier level.
At the top level of pathways modules, genes involved with metabolism were significantly enriched in the oxic sediment. At the functional subcategory level, three pathways within metabolism i. At the functional subcategory level two , the oxic-anoxic treatment was significantly enriched with genes involved in: cell growth and death, signal transduction, translation, replication and repair, glycan biosynthesis and metabolism, and nucleotide metabolism Fig.
The higher resolution analysis of the predicted functional capacities Supplementary Fig. Of the 28 predicted functional pathways that had significantly higher gene counts in the oxic sediments five included genes involved in xenobiotics biodegradation including fluorobenzoate, chlorocyclohexane and chlorobenzene, polycyclic aromatic hydrocarbons, naphthalene, aminobenzoate and the degradation of terpenoids and polyketides.
In contrast, the bacterial communities in the redox-stratified sediments had significantly higher abundance of genes predicted to be involved in purine and pyrimidine nucleic acid metabolism , nitrogen metabolism, carbon fixation pathways and a variety of functional pathways categorised within genetic information processing and cellular processes.
Redox potential was the principal driver of shifts in bacterial community composition and predicted functional capacity. However, these distinctions did not translate into significant differences in terms of sea cucumber growth as previously observed In the present study, the final sea cucumber biomass densities were significantly higher than those achieved in Robinson et al. The growth curves between the studies followed the same pattern, i. Due to facilities access constraints the current trial was terminated prior to attaining statistical significance, however the similarities between the growth profiles give us cause to be confident that, had the trial been run for longer, a significant difference would have been achieved.
The growth rate and final biomass density differences between studies can be attributed to seasonal differences between the respective trials.
The Robinson et al. Temperature is one of the key environmental variables affecting the activity, metabolism and growth rate of marine invertebrates, including H. The longer day lengths coupled with stronger irradiances will have increased photoautotrophic production in the current study relative to Robinson et al. The active circulation of oxygenated seawater through the sediment in the oxic treatment led to the establishment of a microbial community characterised by a higher relative abundance, diversity, richness and evenness, with an enrichment of predicted metabolic and functional potential for bioremediation.
This contrasts the bacterial communities present in the predominately anaerobic sediment of the oxic-anoxic treatment Supplementary Tables 3 and 4. The presence of molecular oxygen is a major factor determining changes in bacterial community structure with consequent impacts on biogeochemical cycles and organic matter mineralization 1 , 13 , 19 , 20 , 21 , Obligate aerobes and microaerophiles require oxygen for energy production and depend on the transfer of electrons to oxygen, which is the final electron acceptor in electron transport-linked oxidative phosphorylation.
All of the bacterial biomarkers in the fully oxic treatment were obligate or facultative aerobes. In the redox-stratified sediments the molecular diffusion of oxygen would have been limited to a depth of a few millimetres below which microbial activity would have been predominately anaerobic 23 , This was supported by the majority of biomarkers being classified as either strict or obligate anaerobes.
Competition between bacteria is based on substrate uptake kinetics and the efficiency with which the substrate is coupled to growth
Bacterial Physiology and Metabolism
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Microbial Physiology & Metabolism
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Microbial Physiology and Metabolism
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