Microbial functioning refers to microbial activity because only the active microorganisms drive biogeochemical processes. Despite the importance of active microorganisms, most methods focus on ...estimating total microbial biomass and fail to evaluate its active fraction. At first, we have described the differences among the active, potentially active, and dormant microbial states in soil and suggested threshold values of parameters for their identification. Secondly, we critically reviewed the ability of a broad range of approaches to estimate and characterize the active and the potentially active microorganisms in soil. Following approaches were evaluated: plate count and microbial cultures; direct microscopy combined with cell staining; ATP, PLFA, DNA and RNA content; microarray analyses; PCR-based approaches; stable isotope probing; soil proteomics, enzymes activity; and various approaches based on respiration and substrate utilization. The “static” approaches, mainly based on the single-stage determination of cell components (ATP, DNA, RNA, and molecular biomarkers), detect well the presence of microorganisms and total biomass, but they fail to evaluate the active part and consequently the functions. In contrast, the dynamic approaches, estimating the changes of these parameters during microbial growth and based on process rates: substrate utilization and product formation, e.g., respiration, help to evaluate active microbial biomass and relate it to specific process rates. Based on a comparison of all approaches for their universality (possibility to analyze active, potentially active and dormant microorganisms), we concluded that 1) direct microscopy with complementary stains, 2) a combination of RNA-based FISH with staining of total microbial biomass, and 3) approaches based on microbial growth were the most advantageous and allowed simultaneous quantitative estimation of active, potentially active, and dormant microorganisms in soil.
The active microorganisms compose only about 0.1–2% of the total microbial biomass and very seldom exceed 5% in soils without input of easily available substrates. Nonetheless, the fraction of potentially active microorganisms (ready to start utilization of available substrates within few hours) is much higher, contributing between 10 and 40% (up to 60%) of the total microbial biomass. Therefore, we emphasize the role of potentially active microorganisms with quick response to fluctuating substrate input in soil microhabitats and hotspots.
The transition from the potentially active to the active state occurs in minutes to hours, but the shift from dormant to active state takes anywhere from hours to days. Despite very fast activation, the reverse process – fading to the potentially active and dormant stage – requires a much longer period and is very different for individual criteria: ATP, DNA, RNA, enzyme production, respiration rates. This leads to further difficulties in the estimation of the active part of microbial community by methods based on these parameters. Consequently, the standardization, further elaboration, and broad application of approaches focused on the portion of active microorganisms in soil and their functions are urgently needed. We conclude that because active microorganisms are the solely microbial drivers of main biogeochemical processes, analyses of the active and potentially active fractions are necessary in studies focused on soil functions.
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•We critically evaluated literature on active soil microorganisms and revealed.•Microorganisms in active and potentially active state: tiny versus large pool.•Threshold parameters for microbial activity state in soil.•Relevance of active microbial fraction in calculations of process rates.•Combinations of dynamic approaches enable to evaluate active microbial biomass.
Enterococci are Gram-positive commensals of the mammalian intestinal tract and harbor intrinsic resistance to broad-spectrum cephalosporins. Disruption of colonization resistance in humans by ...antibiotics allows enterococci to proliferate in the gut and cause disseminated infections.
Enterococci are Gram-positive commensals of the mammalian intestinal tract and harbor intrinsic resistance to broad-spectrum cephalosporins. Disruption of colonization resistance in humans by antibiotics allows enterococci to proliferate in the gut and cause disseminated infections. In this study, we used
Enterococcus faecalis
(EF)-colonized mice to study the dynamics of enterococci, commensal microbiota, and the host in response to systemic ceftriaxone administration. We found that the mouse model recapitulates intestinal proliferation and dissemination of enterococci seen in humans. Employing a ceftriaxone-sensitive strain of enterococci (
E. faecalis
JL308), we showed that increased intestinal abundance is critical for the systemic dissemination of enterococci. Investigation of the impact of ceftriaxone on the mucosal barrier defenses and integrity suggested that translocation of enterococci across the intestinal mucosa was not associated with intestinal pathology or increased permeability. Ceftriaxone-induced alteration of intestinal microbial composition was associated with transient increase in the abundance of multiple bacterial operational taxonomic units (OTUs) in addition to enterococci, for example, lactobacilli, which also disseminated to the extraintestinal organs. Collectively, these results emphasize that ceftriaxone-induced disruption of colonization resistance and alteration of mucosal homeostasis facilitate increased intestinal abundance of a limited number of commensals along with enterococci, allowing their translocation and systemic dissemination in a healthy host.
Cadaver decomposition is a natural phenomenon intimately affected by numerous organisms such as insects, fungi, animals, and bacteria where they use the decaying body as their nutrition source. These ...organisms can be utilized in forensic science to estimate the post-mortem interval (PMI). The post-mortem interval refers to the time that has passed since the death of a person until the body was found. Forensic entomology is one of the popular approaches where successive colonization of insects on cadaver is studied to estimate PMI. However, sometime this method does not provide consistent results due to lack of insect activities during cold environment conditions or when crime scene is indoor. Therefore, a new approach is needed to aid forensic scientists to estimate PMI. Recently, researchers have noted that microbial communities have shown a predictable and clockwise successional pattern on decomposing cadavers and suggested this could be utilized to estimate PMI when this approach is etched with other established methods. The purpose of this review is to summarize some of the studies that have been conducted on the utility of microbial communities in estimating PMI and discuss the role of microbial communities in cadaver decomposition.
Among the different pharmaceuticals present in soil and water ecosystems as micro-contaminants, considerable attention has been paid to antibiotics, since their increasing use and the consequent ...development of multi-resistant bacteria pose serious risks to human and veterinary health. Moreover, once they have entered the environment, antibiotics can affect natural microbial communities. The latter play a key role in fundamental ecological processes, most importantly the maintenance of soil and water quality. In fact, they are involved in biogeochemical cycling and organic contaminant degradation thanks to their large reservoir of genetic diversity and metabolic capability. When antibiotics occur in the environment, they can hamper microbial community structure and functioning in different ways and have both direct (short-term) and indirect (long-term) effects on microbial communities. The short-term ones are bactericide and bacteriostatic actions with a consequent disappearance of some microbial populations and their ecological functioning. The indirect impact includes the development of antibiotic resistant bacteria and in some cases bacterial strains able to degrade them by metabolic or co-metabolic processes. Biodegradation makes it possible to completely remove a toxic compound from the environment if it is mineralized.
Several factors can influence the significance of such direct and indirect effects, including the antibiotic's concentration, the exposure time, the receiving ecosystem (e.g. soil or water) and the co-occurrence of other antibiotics and/or other contaminants.
This review describes the current state of knowledge regarding the effects of antibiotics on natural microbial communities in soil and water ecosystems.
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•Antibiotics affect the diversity of natural bacterial communities.•Biodegradation is a homeostatic response by the natural microbial community.•Antibiotics and antibiotic resistance genes (ARGs) are emerging contaminants.•ARGs are naturally found in the chromosomes of some environmental bacteria.•Antibiotics are signals that trigger microbial community functioning.
Profiling of microbial communities in environmental samples often utilizes phospholipid fatty acid (PLFA) analysis. This method has been used for more than 35 years and is still popular as a means to ...characterize microbial communities in a diverse range of environmental matrices. This review examines the various recent applications of PLFA analysis in environmental studies with specific reference to the interpretation of the PLFA results. It is evident that interpretations of PLFA results do not always correlate between different investigations. These discrepancies in interpretation and their subsequent applications to environmental studies are discussed. However, in spite of limitations to the manner in which PLFA data are applied, the approach remains one with great potential for improving our understanding of the relationship between microbial populations and the environment. This review highlights the caveats and provides suggestions towards the practicable application of PLFA data interpretation.
The metabolic activities of microbial communities play a defining role in the evolution and persistence of life on Earth, driving redox reactions that give rise to global biogeochemical cycles. ...Community metabolism emerges from a hierarchy of processes, including gene expression, ecological interactions, and environmental factors. In wild communities, gene content is correlated with environmental context, but predicting metabolite dynamics from genomes remains elusive. Here, we show, for the process of denitrification, that metabolite dynamics of a community are predictable from the genes each member of the community possesses. A simple linear regression reveals a sparse and generalizable mapping from gene content to metabolite dynamics for genomically diverse bacteria. A consumer-resource model correctly predicts community metabolite dynamics from single-strain phenotypes. Our results demonstrate that the conserved impacts of metabolic genes can predict community metabolite dynamics, enabling the prediction of metabolite dynamics from metagenomes, designing denitrifying communities, and discovering how genome evolution impacts metabolism.
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•Metabolite fluxes in microbial communities are predictable from individual genotypes•A diverse collection of 79 bacterial isolates was sequenced and phenotyped•Gene presence and absence predict metabolic phenotypes of isolates via regression•A consumer-resource model predicts community metabolite fluxes from phenotypes
The presence or absence of specific genes within communities of wild bacterial isolates is sufficient to predict community-level metabolite dynamics without detailed knowledge of pathway regulation or complex ecological processes.
Micro-and nano-plastics (MNPs) (size < 5 mm/<100 nm) epitomize one of the emergent environmental pollutants with its existence all around the globe. Their high persistence nature and release of ...chemicals/additives used in synthesis of plastics materials may pose cascading impacts on living organism across the globe. Natural connectivity of all the environmental compartments (terrestrial, aquatic, and atmospheric) leads to migration/dispersion of MNPs from one compartment to others. Nevertheless, the information on dispersion of MNPs across the environmental compartments and its possible impacts on living organisms are still missing. This review first acquaints with dispersion mechanisms of MNPs in the environment, its polymeric/oligomeric and chemical constituents and then emphasized its impacts on living organism. Based on the existing knowledge about the MNPs’ constituent and its potential impacts on the viability, development, lifecycle, movements, and fertility of living organism via several potential mechanisms, such as irritation, oxidative damage, digestion impairment, tissue deposition, change in gut microbial communities’ dynamics, impaired fatty acid metabolism, and molecular damage are emphasized. Finally, at the end, the review provided the challenges associated with remediation of plastics pollutions and desirable strategies, policies required along with substantial gaps in MNPs research were recommended for future studies.
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•This review first acquaints with dispersion mechanisms of micro-nano plastics in the environment.•Reviewed polymeric and chemicals constituents of micro-nano plastics and its impact on living organisms.•Plastics pollutions, its remediation strategies, challenges, and policies are discussed.•Substantial gaps in micro-nano plastics research were recommended for future studies.
How soil processes such as carbon cycling will respond to future climate change depends on the responses of complex microbial communities, but most ecosystem models assume that microbial functional ...responses are resilient and can be predicted from simple parameters such as biomass and temperature. Here, we consider how historical contingencies might alter those responses because function depends on prior conditions or biota. Functional resilience can be driven by physiological, community or adaptive shifts; historical contingencies can result from the influence of historical environments or a combination of priority effects and biotic resistance. By modelling microbial population responses to environmental change, we demonstrate that historical environments can constrain soil function with the degree of constraint depending on the magnitude of change in the context of the prior environment. For example microbial assemblages from more constant environments were more sensitive to change leading to poorer functional acclimatisation compared to microbial assemblages from more fluctuating environments. Such historical contingencies can lead to deviations from expected functional responses to climate change as well as local variability in those responses. Our results form a set of interrelated hypotheses regarding soil microbial responses to climate change that warrant future empirical attention.
This study aims to investigate the effects of long-term nicosulfuron residue on an herbicide factory ecosystem. High-throughput sequencing was used to investigate the environmental microbial ...community structure and interactions. The results showed that the main contributor to the differences in the microbial community structure was the sample type, followed by oxygen content, pH and nicosulfuron residue concentration. Regardless of the presence or absence of nicosulfuron, soil, sludge, and sewage were dominated by groups of Bacteroidetes, Actinobacteria, and Proteobacteria. Long-term exposure to nicosulfuron increased alpha diversity of bacteria and archaea but significantly decreased the abundance of Bacteroidetes and Acidobateria compared to soils without nicosulfuron residue. A total of 81 possible nicosulfuron-degrading bacterial genera, e.g., Rhodococcus, Chryseobacterium, Thermomonas, Stenotrophomonas, and Bacillus, were isolated from the nicosulfuron factory environmental samples through culturomics. The co-occurrence network analysis indicated that the keystone taxa were Rhodococcus, Stenotrophomonas, Nitrospira, Terrimonas, and Nitrosomonadaceae_MND1. The strong ecological relationship between microorganisms with the same network module was related to anaerobic respiration, the carbon and nitrogen cycle, and the degradation of environmental contaminants. Synthetic community (SynCom), which provides an effective top-down approach for the critical degradation strains obtained, enhanced the degradation efficiency of nicosulfuron. The results indicated that Rhodococcus sp. was the key genus in the environment of long-term nicosulfuron exposure.
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•Nicosulfuron-degrading strains in chronically contaminated soil become dominant.•Long-term nicosulfuron residue increased the alpha diversity of soil microorganisms.•A synthetic community with Rhodococcus sp. had enhanced degradation efficiency.
The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the ...coevolution of new sequencing platforms and new software tools allows data acquisition and analysis on an unprecedented scale. Here we report the next stage in this coevolutionary arms race, using the Illumina GAIIx platform to sequence a diverse array of 25 environmental samples and three known "mock communities" at a depth averaging 3.1 million reads per sample. We demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature (notably, the saline/nonsaline split in environmental samples and the split between host-associated and free-living communities). We also demonstrate that 2,000 Illumina single-end reads are sufficient to recapture the same relationships among samples that we observe with the full dataset. The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution.
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