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Molecular Methods for Assessing Microbial Corrosion and Souring Potential in Oilfield Operations
Published in Kenneth Wunch, Marko Stipaničev, Max Frenzel, Microbial Bioinformatics in the Oil and Gas Industry, 2021
Gloria N. Okpala, Rita Eresia-Eke, Lisa M. Gieg
Mouser et al. (2016) overviewed a number of studies using MMM approaches, including metagenomics, to understand microbial functioning in these subsurface environments. For example, Mohan et al. (2014) used a metagenome approach to determine microbial community compositions and potential functions from a Marcellus shale natural gas well. The authors analyzed the metagenome of hydraulic fracturing source water along with produced water (flowback water) after day 1 and day 9. The microorganisms changed notably, with members of the order Rhodobacterales dominating in both the source water and day one produced water but decreasing in the day 9 produced water. There was also an increase in members of the order Thermoanaerobacterales in the day 1 produced water, but this decreased in relative abundance by day 9. However, Gammaproteobacteria, which constituted a minor fraction of the source water community, were present at over 50% relative abundance in the day 9 produced water. Shifts were also found in functional categories of metagenomes. There was an increase in carbohydrate metabolism genes in day 9 produced water, which suggested the ability of the microbial community to use available carbon sources from the shale formation or those added in fracturing fluids. Stress response genes (such as for heat shock or acid, periplasmic, or osmotic stress) were primarily associated with Vibrionales and Altermonadales, while genes involved in sulfur metabolism were associated with Vibrionales and Bacteriodales in the day 9 produced water. This kind of shotgun metagenomic analysis showed the emergence of distinct bacterial taxa and functionality as the result of changes to the environment, providing information to operators that may guide decision-making with respect to biocide control treatment options, and source water and wastewater management.
Long-term dynamics of the bacterial community in a Swedish full-scale wastewater treatment plant
Published in Environmental Technology, 2019
Nils Johan Fredriksson, Malte Hermansson, Britt-Marie Wilén
To characterize the bacterial community in the activated sludge, 16S rRNA gene libraries were generated from three samples collected at different times: early winter (11/07/2003), late winter (02/26/2004) and summer (07/15/2004). The libraries included 49 (11/07/2003), 65 (02/26/2004) and 63 (07/15/2004) sequences, and the estimated coverage at species level was 66%, 30% and 58%. In all three samples, the retrieved sequences were dominated by Proteobacteria, with Alphaproteobacteria being the most abundant (Figure 1, panel A). However, within the phyla, there were some differences between the samples (Figure 1, panel B). Most Alphaproteobacteria sequences in all three libraries were classified as Rhizobiales or Rhodobacterales, but the proportions of the two orders varied. For example, the order Rhizobiales was nearly absent in the sample collected 02/26/2004, but it was the most abundant in the sample from 07/15/2004. The Rhodobacterales sequences were classified as Rhodobacteraceae, which include heterotrophs and phototrophs found in many different environments, including freshwater and seawater [43], clinical samples [44], sediments [45], soil [46], wastewater ditches [47] and activated sludge [48]. The sequences of Rhizobiales were classified as Beijerinckiaceae (which are nitrogen-fixing heterotrophs found in soil [49,50]), Hyphomicrobiaceae (heterotrophic and methylotrophic bacteria found in soil [51,52]) and Methylocystaceae (type II methanotrophs isolated from wetlands [53] and aquifers [54]). Most Alphaproteobacteria found at the Rya WWTP were highly similar to sequences retrieved from other environments, such as bioreactors, soils, sediments, human skin and digestive tract (See Table S2, BLAST search).
Low cost and renewable H2S-biofilter inoculated with Trichoderma harzianum
Published in Environmental Technology, 2022
Muriel Chaghouri, Cédric Gennequin, Lucette Haingomalala Tidahy, Fabrice Cazier, Edmond Abi–Aad, Etienne Veignie, Catherine Rafin
However, several bacterial species were also identified in the biofilter. These bacteria were not initially inoculated in the bioreactor but are the result of spontaneous colonization caused by a partially non-sterile environment. The species mentioned in Figure 4 represent 90% of the bacteria installed in the bioreactor. Agrobacterium, Paracoccus, Ralstonia, Roseomonas, Curtobacterium, Methylobacterium, Burkhoderia, and Escherichia represent respectively 55, 10, 9, 6, 4, 2, 1, 1% of the bacterial relative abundance in the biofilter. Several of these species have been already reported in previous studies of H2S production or degradation. Some have even been used for biofilter or biotrickling filters for H2S elimination. For example, Paracoccus (Rhodobacteraceae, Rhodobacterales, Alphaproteobacteria, Proteobacteria), has been used as a sulphur-oxidizing bacteria in many lab-scale biofilters and biotrickling filters for H2S removal, eliminating up to 96% of the introduced H2S [57,58]. Methylobacterium (Methylobacteriaceae, Rhizobiales, Alphaproteobacteria, Proteobacteria) is also a well-known sulphur-oxidizing bacteria that can transform reduced sulphur such as hydrogen sulphide and methylated sulphur compounds into sulphate [59,60]. On the other hand, Agrobacterium (Rhizobiaceae, Rhizobiales, Alphaproteobacteria, Proteobacteria) can survive in an H2S-rich environment as well as oxidize and produce H2S [61–63]. Although this bacterium has shown great promise in H2S removal, it has not yet been used for sulphur biopurification. Burkholderia (Burkholderiaceae, Burkholderiales, Betaproteobacteria, Proteobacteria) has also been used for lab-scale biological oxidation of H2S [64,65]. Finally, Ralstonia (Oxalobacteraceae, Burkholderiales, Betaproteobacteria, Proteobacteria) and Curtobacterium (Microbacteriaceae, Actinomycetales, Actinobacteridae, Actinobacteria) have already been linked to the production of H2S from S-amino acids such as cysteine and cystine as well as inorganic Na2S2O3– [66–69]. This would explain how these microorganisms managed to survive in an environment containing H2S. In reality, more species of bacteria have probably been introduced into the bioreactor, but only the bacteria associated with H2S (H2S-resistant, S-oxidizing, or H2S-producing) were able to survive in this extreme environment and form an H2S-oriented microbiome. The spontaneous development of a bacterial and fungal consortium explains the efficiency of this H2S-design biofilter. Even though the fungal and bacterial impact on H2S-removal cannot be dissociated, it is important to mention that 65% of the microbial population is the selected and inoculated T. harzianum based on gDNA content.