Functional Response of MBR Microbial Consortia to Substrate Stress as Revealed by Metaproteomics

Salerno, Carlo; Berardi, Giovanni; Laera, Giuseppe; Pollice, Alfieri

doi:10.1007/s00248-019-01360-4

Cited by 13 publications

(4 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Single‐cell transcriptomics is a high‐resolution approach to generating knowledge of regulatory processes based on single cells (Rich‐Griffin et al, 2020), but it is rarely used in riverine microbial abundance and diversity studies (Figure S3). Metaproteomic analyses are more connected with microbial activity than metatranscriptomic analyses (Salerno et al, 2019); however, the high cost prevents the wide application of the former. Additionally, stable‐isotope probing (SIP) based on DNA or RNA is an ideal tool to investigate active microbial populations with specific functions and has been increasingly employed to study riverine microbes (Kowalczyk et al, 2015; Pepe‐Ranney et al, 2016; Figure S3).…”

Section: Technologies Used To Study River Microorganismsmentioning

confidence: 99%

Microbial abundance and diversity investigations along rivers: Current knowledge and future directions

et al. 2021

WIREs Water

View full text Add to dashboard Cite

Microbial abundance and diversity in river ecosystems are being increasingly investigated, yet a synthesized understanding is still lacking. Here, studies of microbial abundance and diversity along global rivers are systematically reviewed based on 814 investigations performed across 8376 sites. We found that riverine microbial investigations are extremely heterogeneous regarding the spatiotemporal distribution of the sampling sites, the environmental media concerned, the microbial groups and indices targeted, the methods used, and the physicochemical properties examined. More than 72.23% of the studies were performed in the last 8 years, with most studies conducted in Europe, China, and the United States, while other regions were poorly investigated. Most studies have examined microbes in water, but very few studies have systematically investigated microbes in water, sediments, and riparian soils. Bacteria are the most studied microbial taxonomic groups; microbes with resistance genes and nitrogen cycling genes are the most studied microbial functional groups.High-throughput sequencing has greatly expanded our understanding of microbial diversity along rivers. Nevertheless, the ecological implications of microbial diversity are still poorly understood. Regarding physicochemical properties, researchers tend to examine environmental parameters that are critical for shaping microbial communities, such as pH, nitrogen, and phosphorus. Future research should pay more attention to rivers that have not been well studied, especially large rivers. Additionally, microbial studies along rivers should be conducted in a more systematic way, taking the underinvestigated environmental media, microbial groups, microbial indices, and physicochemical properties into consideration. Advanced microbiology techniques, such as multiple omics technologies, should be increasingly applied.

show abstract

Section: Technologies Used To Study River Microorganismsmentioning

confidence: 99%

Microbial abundance and diversity investigations along rivers: Current knowledge and future directions

et al. 2021

WIREs Water

View full text Add to dashboard Cite

show abstract

“…Metatranscriptomics and metaproteomics are powerful methods to infer if the microbes are performing as expected. Metaproteomic studies of MBR communities were performed to understand fouling (Zhou et al, 2015) or the effect of substrate stress (Salerno et al, 2019).…”

Section: Microbial Community Analysismentioning

confidence: 99%

Genome sequencing as a new window into the microbial community of membrane bioreactors – A critical review

Nguyen

Commault

Ralph

et al. 2020

Science of The Total Environment

View full text Add to dashboard Cite

“…A metaproteomic approach is more often used to characterize the functionality and to identify novel functional proteins and their respective metabolic pathways in those bioreactors [30][31][32]. Moreover, the technique can also be used as a taxonomical identification tool [33]. However, metaproteomics has not yet been applied to determine microbial abundancies in (de)nitrification bioreactors.…”

Section: Introductionmentioning

confidence: 99%

Metaproteomics, Heterotrophic Growth, and Distribution of Nitrosomonas europaea and Nitrobacter winogradskyi after Long-Term Operation of an Autotrophic Nitrifying Biofilm Reactor

Mastroleo

Arnau

Verbeelen

et al. 2022

Applied Microbiology

View full text Add to dashboard Cite

Bioregenerative life support systems (BLSS) are currently in development to tackle low recovery efficiencies, high energy demands, as well as food, water, and oxygen production challenges through the regeneration of nutrients from waste streams. The MELiSSA pilot plant has been developed as a testbed for regenerative life support system bioreactor operation and characterization. As nitrogen is a vital resource in such systems, we studied the functional composition of a new packed-bed nitrifying bioreactor inoculated with a co-culture of Nitrosomonas europaea (ATCC 25978) and Nitrobacter winogradskyi (ATCC 25391). After 840 days of autotrophic continuous cultivation, the packed-bed was sampled at five vertical positions, each with three horizontal positions, and the biomass at each position was characterized via qPCR, 16S amplicon sequencing, and liquid chromatography tandem mass spectrometry. The total number of cells within the different sections fluctuated around 8.95 ± 5.10 × 107 cells/mL of beads. Based on 16S amplicons and protein content, N. europaea and N. winogradskyi constituted overall 44.07 ± 11.75% and 57.53 ± 12.04% of the nitrifying bioreactor, respectively, indicating the presence of a heterotrophic population that, even after such a long operation time, did not affect the nitrification function of the bioreactor. In addition, DNA-based abundance estimates showed that N. europaea was slightly more abundant than N. winogradskyi, whereas protein-based abundance estimates indicated a much higher abundance of N. europaea. This highlights that single-method approaches need to be carefully interpreted in terms of overall cell abundance and metabolic activity.

show abstract

Functional Response of MBR Microbial Consortia to Substrate Stress as Revealed by Metaproteomics

Cited by 13 publications

References 40 publications

Microbial abundance and diversity investigations along rivers: Current knowledge and future directions

Microbial abundance and diversity investigations along rivers: Current knowledge and future directions

Genome sequencing as a new window into the microbial community of membrane bioreactors – A critical review

Metaproteomics, Heterotrophic Growth, and Distribution of Nitrosomonas europaea and Nitrobacter winogradskyi after Long-Term Operation of an Autotrophic Nitrifying Biofilm Reactor

Contact Info

Product

Resources

About