The Challenges of Studying the Anaerobic Microbial World

Mori, Koji; Kamagata, Yoichi

doi:10.1264/jsme2.me2904rh

Cited by 31 publications

(20 citation statements)

References 52 publications

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“…It is difficult to conclude their possible function in the ecosystem owing to the absence of cultured representatives of these phyla. Planctomycetes are anaerobic ammonium oxidizing bacterium which can contribute to N and C cycling in the soil [57]. A higher abundance of these bacteria in M-and MS-containing soil is due to a large amount of N and C sources than CK-and S-amended soil in the second phase [23].…”

Section: Discussionmentioning

confidence: 99%

Effect of Sugarcane Straw and Goat Manure on Soil Nutrient Transformation and Bacterial Communities

et al. 2018

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Crop residue and animal manure as a soil amendment have been recognized as a feasible agricultural practice owing to its contribution in improving the soil fertility (SF). The primary advantages of this practice are determined by the activities of soil microorganisms. However, goat manure (M), sugarcane straw (S), and goat manure plus straw (MS) amendments influence soil bacteria, their activities, and SF in clay-loam soil remains undefinable. Therefore, this study distinguished the efficacy of M, MS, and S amendment on soil enzyme activities and the availability of nutrients, including various bacterial populations in clay-loamy soil with respect to two different phases (50 and 100 days). In order to analyze the bacterial structure and their activities, we employed high-throughput sequencing (HTS) and soil enzyme activity (SEA) tests. Soil amended with M and MS not only significantly enhanced nutrient availability, including C, P, and N, soil pH, as well as SEA for C and N cycles in both phases. Additionally, the increase in nutrient availability was greater in M-and MS-amended soils in the second phase (100 days) compared to the M-and S-amended soils in the first phase (50 days). Moreover, plant growth promoting and lignocellulose degrading bacterial genera were enhanced under M-and MS-amended soil compared to S-amended soil in both phases. Distance-based redundancy analysis (dbRDA) showed that soil pH, carbon-nitrogen ratio (C:N), and nitrates (NO 3 − )were inducing the fewest changes, while total nitrogen (TN), total carbon (TC), available nitrogen (AN), available phosphorus (AP), total phosphorus (TP), available potassium (AK), and ammonium (NH 4 + )were the main operators in terms of change in bacterial populations. In general, we observed that M and MS are better amendment sources as compared to S amendment in order to enhance the SF in the clay-loamy soil in both phases, but greater fertility was exhibited in the second phase.

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Section: Discussionmentioning

confidence: 99%

Effect of Sugarcane Straw and Goat Manure on Soil Nutrient Transformation and Bacterial Communities

et al. 2018

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“…Detection of anaerobic bacteria by cultures can pose technical difficulties and is known to have suboptimal diagnostic sensitivity. 22,23 We, therefore, strongly suspect that anaerobes are underreported in the present series and that their prevalence in 31% of infections should be viewed as a lower limit. Studies using polymerase chain reaction (PCR) as a comparison have shown it to have significantly greater sensitivity, though often at the expense of specificity.…”

Section: Frequency Of Microbial Species In Surgical Site Infectionsmentioning

confidence: 74%

“…Detection of anaerobic bacteria by cultures can pose technical difficulties and is known to have suboptimal diagnostic sensitivity . We, therefore, strongly suspect that anaerobes are underreported in the present series and that their prevalence in 31% of infections should be viewed as a lower limit.…”

Section: Discussionmentioning

confidence: 86%

Identification of infectious species after resection of soft‐tissue sarcomas

Ramsey

Jones

Weiss

et al. 2019

Journal of Surgical Oncology

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Background Pathogenic species in deep tissue infections after soft‐tissue sarcoma (STS) resection is largely unstudied, particularly the role of anaerobic bacteria, risks factors for those pathogens, and the time course of infection presentation. Methods Retrospective analysis of 64 patients requiring operative debridement for deep tissue infection after STS resection was undertaken to identify infectious species and study risk factors for anaerobic infections. Kaplan–Meier methods examined the time course of infection presentation. Results STS subtypes were most commonly pleomorphic STS, myxofibrosarcoma, and undifferentiated STS. Staphylococcus aureus was the most common organism isolated (56%). Twenty (31%) infections were positive for ≥1 anaerobic organism. Twelve gram‐positive and 10 gram‐negative aerobic organisms were isolated. Most (90%) anaerobic‐containing infections were polymicrobial, vs 52% of purely aerobic infections. No significant risk factors for anaerobic infections were identified. Median time from tumor resection until debridement was significantly greater for anaerobic infections (54.5 days) than for purely aerobic infections (29.5 days; P = 0.004), a difference so pronounced that using “presentation after 53 days” as a proxy for the presence of anaerobic pathogens had an accuracy of 81%. Conclusions Because polymicrobial and anaerobic bacterial infections are common, we strongly support antibiotic use with anaerobic coverage at debridement, particularly for infections presenting later.

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“…(56, 57). In contrast, no transconjugants were recovered from the anaerobic microcosms, most likely because such HGT events took place with fastidious bacteria highly prevalent in anaerobic environments (58), and these bacteria cannot be easily cultivated. Similarly, after 120 h of aerobic microcosm establishment, transconjugants were no longer recovered from the aerobic sludge (Fig.…”

Section: Discussionmentioning

confidence: 99%

Fate and Persistence of a Pathogenic NDM-1-Positive Escherichia coli Strain in Anaerobic and Aerobic Sludge Microcosms

Mantilla‐Calderon

Hong

2017

Appl Environ Microbiol

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The presence of emerging biological pollutants in treated wastewater effluents has gained attention due to increased interest in water reuse. To evaluate the effectiveness of the removal of such contaminants by the conventional wastewater treatment process, the fate and decay kinetics of NDM-1-positive Escherichia coli strain PI7 and its plasmid-encoded antibiotic resistance genes (ARGs) were assessed in microcosms of anaerobic and aerobic sludge. Results showed that E. coli PI7 decayed at a significantly lower rate under anaerobic conditions. Approximate half-lives were 32.4 ± 1.4 h and 5.9 ± 0.9 h in the anaerobic and aerobic microcosms, respectively. In the aerobic microcosms, after 72 h of operation, E. coli PI7 remained detectable, but no further decay was observed. Instead, 1 in every 10,000 E. coli cells was identified to be recalcitrant to decay and persist indefinitely in the sludge. ARGs associated with the E. coli PI7 strain were detected to have transferred to other native microorganisms in the sludge or were released to the liquid fraction upon host decay. Extracellular DNA quickly degraded in the liquid fraction of the aerobic sludge. In contrast, no DNA decay was detected in the anaerobic sludge water matrix throughout the 24-h sampling period. This study suggests an increased likelihood of environmental dispersion of ARGs associated with anaerobically treated wastewater effluents and highlights the potential importance of persister cells in the dissemination of E. coli in the environment during reuse events of treated wastewater.IMPORTANCE This study examines the decay kinetics of a pathogenic and antibiotic resistant strain of Escherichia coli in microcosms simulating biological treatment units of aerobic and anaerobic sludge. The results of this study point at a significantly prolonged persistence of the E. coli and the associated antibiotic resistance gene in the anaerobic sludge. However, horizontal transfer of the plasmid encoding the antibiotic resistance gene was detected in the aerobic sludge by a cultivation method. A subpopulation of persister E. coli cells was also detected in the aerobic sludge. The findings of this study suggest potential areas of concern arising from pathogenic and antibiotic-resistant E. coli during both anaerobic and aerobic sludge treatment processes.

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The Challenges of Studying the Anaerobic Microbial World

Cited by 31 publications

References 52 publications

Effect of Sugarcane Straw and Goat Manure on Soil Nutrient Transformation and Bacterial Communities

Effect of Sugarcane Straw and Goat Manure on Soil Nutrient Transformation and Bacterial Communities

Identification of infectious species after resection of soft‐tissue sarcomas

Fate and Persistence of a Pathogenic NDM-1-Positive Escherichia coli Strain in Anaerobic and Aerobic Sludge Microcosms

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