Methylotrophs and Hydrocarbon-Degrading Bacteria Are Key Players in the Microbial Community of an Abandoned Century-Old Oil Exploration Well

Rojas‐Gätjens, Diego; Fuentes-Schweizer, Paola; Rojas-Jiménez, Keilor; Pérez‐Pantoja, Danilo; Avendaño, Roberto; Alpízar, Randall; Coronado-Ruíz, Carolina; Chavarría, Max

doi:10.1007/s00248-021-01748-1

Cited by 15 publications

(23 citation statements)

References 100 publications

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“…The type I Methylobacter -related group were found to be indicator species above a typical onshore oil and gas reservoir, whereas type II methanotrophic Methylosinus was indicative of the active population in the background soils [ 3 ]. Similar results have been observed in abandoned oil exploration wells [ 13 ] and terrestrial natural gas seeps [ 14 ]. However, the opposite results have also been reported by other petroleum explorationists [ 15 , 16 ], who detected anomalies of type II Methylocystis and Methylosinus in Chinese oilfields.…”

Section: Resultssupporting

confidence: 87%

Identifying Active Rather than Total Methanotrophs Inhabiting Surface Soil Is Essential for the Microbial Prospection of Gas Reservoirs

Xu,

Tao,

et al. 2024

Microorganisms

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Methane-oxidizing bacteria (MOB) have long been recognized as an important bioindicator for oil and gas exploration. However, due to their physiological and ecological diversity, the distribution of MOB in different habitats varies widely, making it challenging to authentically reflect the abundance of active MOB in the soil above oil and gas reservoirs using conventional methods. Here, we selected the Puguang gas field of the Sichuan Basin in Southwest China as a model system to study the ecological characteristics of methanotrophs using culture-independent molecular techniques. Initially, by comparing the abundance of the pmoA genes determined by quantitative PCR (qPCR), no significant difference was found between gaswell and non-gaswell soils, indicating that the abundance of total MOB may not necessarily reflect the distribution of the underlying gas reservoirs. 13C-DNA stable isotope probing (DNA-SIP) in combination with high-throughput sequencing (HTS) furthermore revealed that type II methanotrophic Methylocystis was the absolutely predominant active MOB in the non-gas-field soils, whereas the niche vacated by Methylocystis was gradually filled with type I RPC-2 (rice paddy cluster-2) and Methylosarcina in the surface soils of gas reservoirs after geoscale acclimation to trace- and continuous-methane supply. The sum of the relative abundance of RPC-2 and Methylosarcina was then used as specific biotic index (BI) in the Puguang gas field. A microbial anomaly distribution map based on the BI values showed that the anomalous zones were highly consistent with geological and geophysical data, and known drilling results. Therefore, the active but not total methanotrophs successfully reflected the microseepage intensity of the underlying active hydrocarbon system, and can be used as an essential quantitative index to determine the existence and distribution of reservoirs. Our results suggest that molecular microbial techniques are powerful tools for oil and gas prospecting.

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Section: Resultssupporting

confidence: 87%

Identifying Active Rather than Total Methanotrophs Inhabiting Surface Soil Is Essential for the Microbial Prospection of Gas Reservoirs

Xu,

Tao,

et al. 2024

Microorganisms

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“…For total DNA extraction of sloth hair, the samples were proceeded as described by Rojas‐Gätjens et al . (2022) with some modifications. Briefly, hair samples were cut with sterile scissors into smaller pieces.…”

Section: Methodsmentioning

confidence: 99%

“…Amplicon sequencing data were analysed using the DADA2 pipeline (version 1.12), as described by Rojas‐Gätjens et al . (2022). Briefly, reads were quality‐filtered, deduplicated, and amplicon sequence variant (ASV), a higher‐resolution analogue of the traditional operational taxonomic unit, was inferred.…”

Section: Methodsmentioning

confidence: 99%

Antibiotic‐producing Micrococcales govern the microbiome that inhabits the fur of two‐ and three‐toed sloths

Rojas‐Gätjens¹,

Valverde-Madrigal²,

Rojas-Jiménez

et al. 2022

Environmental Microbiology

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Summary Sloths have a dense coat on which insects, algae and fungi coexist in a symbiotic relationship. This complex ecosystem requires different levels of controls; however, most of these mechanisms remain unknown. We investigated the bacterial communities inhabiting the hair of two‐ (Choloepus Hoffmanni) and three‐toed (Bradypus variegatus) sloths and evaluated their potential for producing antibiotic molecules capable of exerting control over the hair microbiota. The analysis of 16S rRNA amplicon sequence variants revealed that the communities in both host species are dominated by Actinobacteriota and Firmicutes. The most abundant genera were Brevibacterium, Kocuria/Rothia, Staphylococcus, Rubrobacter, Nesterenkonia and Janibacter. Furthermore, we isolated nine strains of Brevibacterium and Rothia capable of producing substances that inhibited the growth of common mammalian pathogens. The analysis of the biosynthetic gene clusters of these nine isolates suggests that the pathogen‐inhibitory activity could be mediated by the presence of siderophores, terpenes, beta‐lactones, Type III polyketide synthases, ribosomally synthesized and post‐translationally modified peptides, non‐alpha poly‐amino acids like e‐Polylysine, ectoine or non‐ribosomal peptides. Our data suggest that Micrococcales that inhabit sloth hair could have a role in controlling microbial populations in that habitat, improving our understanding of this highly complex ecosystem.

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“…Specifically, bacteria belonging to genera Pseudomonas ( 3 ) and Acinetobacter ( 4 ) have shown potential to degrade alkanes and aromatic hydrocarbons ( 5 , 6 ). Here, we report the genomic sequencing of three strains retrieved from an abandoned old-century oil exploration well, located in the Cahuita National Park, Costa Rica, which is characterized by a continuous efflux of methane and the presence of a complex mixture of hydrocarbons ( 7 ). Sampling details and isolation methods are described by Rojas-Gätjens et al ( 7 ).…”

Section: Announcementmentioning

confidence: 99%

“…Here, we report the genomic sequencing of three strains retrieved from an abandoned old-century oil exploration well, located in the Cahuita National Park, Costa Rica, which is characterized by a continuous efflux of methane and the presence of a complex mixture of hydrocarbons ( 7 ). Sampling details and isolation methods are described by Rojas-Gätjens et al ( 7 ). Such microorganisms were identified as one strain of Pseudomonas sp.…”

Section: Announcementmentioning

confidence: 99%

Draft genome sequence of three hydrocarbon-degrading Pseudomonadota strains isolated from an abandoned century-old oil exploration well

Camacho,

Mesén-Porras,

Rojas-Gätjens

et al. 2024

Microbiol Resour Announc

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We present genome sequences of three Pseudomonadota strains isolated from an abandoned century-old oil exploration well. A Pseudomonas sp. genome showed a size of 5,378,420 bp, while Acinetobacter genomes sized 3,522,593 and 3,864,311 bp. Genomes included catabolic genes for benzoate, 4-hydroxybenzoate, salicylate, vanillate, indoleacetate, anthranilate, n -alkanes, 4-hydroxyphenylacetate, phenylacetate, among others.

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Methylotrophs and Hydrocarbon-Degrading Bacteria Are Key Players in the Microbial Community of an Abandoned Century-Old Oil Exploration Well

Cited by 15 publications

References 100 publications

Identifying Active Rather than Total Methanotrophs Inhabiting Surface Soil Is Essential for the Microbial Prospection of Gas Reservoirs

Identifying Active Rather than Total Methanotrophs Inhabiting Surface Soil Is Essential for the Microbial Prospection of Gas Reservoirs

Antibiotic‐producing Micrococcales govern the microbiome that inhabits the fur of two‐ and three‐toed sloths

Draft genome sequence of three hydrocarbon-degrading Pseudomonadota strains isolated from an abandoned century-old oil exploration well

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