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PubMed2026

Transmission dynamics and driving mechanisms of antibiotic resistance genes through a chronosequence of saline-sodic rice cultivation.

Rice cultivation reclaims saline-sodic soils and improves fertility, but may also promote antibiotic resistance genes (ARGs) accumulation and horizontal transfer, posing ecological risks. This study investigated long-term co-evolution of soil properties, microbial communities, ARGs, and mobile genetic elements (MGEs) across a 1-78 year cultivation chronosequence in saline-sodic fields. Results indicated that prolonged cultivation effectively alleviated soil salinization and increased fertility. Microbial communities shifted directionally, with functional taxa enriched, while opportunistic pathogen-containing genera peaked during 5-20 years. ARGs abundance and diversity increased markedly after five years and peaked at 10-20 years. Multidrug efflux pump genes persisted throughout the chronosequence, whereas aminoglycoside resistance genes declined after 30 years. MGEs activity increased over time and was significantly correlated with key ARGs. Path analysis identified improved soil properties as the primary direct driver of ARGs accumulation, while cultivation-induced declines in microbial diversity indirectly promoted ARGs dissemination by weakening the community's suppression of MGEs-mediated horizontal transfer. Collectively, long-term rice cultivation not only ameliorated saline-sodic soils but also created a dynamic, stage-specific resistome, with the 5-20 year period representing a critical risk window for ARGs propagation. These findings highlight the need to integrate ARGs monitoring into soil health assessments for sustainable management of reclaimed saline-sodic lands.

Oryza↗
PubMed2002

Airway mucus: its components and function.

The airway surface liquid (ASL), often referred to as mucus, is a thin layer of fluid covering the luminal surface of the airway. The major function of mucus is to protect the lung through mucociliary clearance against foreign particles and chemicals entering the lung. The mucus is comprised of water, ions, and various kinds of macromolecules some of which possess the protective functions such as anti-microbial, anti-protease, and anti-oxidant activity. Mucus glycoproteins or mucins are mainly responsible for the viscoelastic property of mucus, which is crucial for the effective mucociliary clearance. There are at least eight mucin genes identified in the human airways, which will potentially generate various kinds of mucin molecules. At present, neither the exact structures of mucin proteins nor their regulation are understood although it seems likely that different types of mucins are involved in different functions and might also be associated with certain airway diseases. The fact that mucins are tightly associated with various macromolecules present in ASL seems to suggest that the defensive role of ASL is determined not only by these individual components but rather by a combination of these components. Collectively, mucins in ASL may be compared to aircraft carriers carrying various types of weapons in defense of airbome enemies.

Animals↗
PubMed2006

Impact of river overflowing on trace element contamination of volcanic soils in south Italy: part II. Soil biological and biochemical properties in relation to trace element speciation.

The effect of heavy metal contamination on biological and biochemical properties of Italian volcanic soils was evaluated in a multidisciplinary study, involving pedoenvironmental, micromorphological, physical, chemical, biological and biochemical analyses. Soils affected by recurring river overflowing, with Cr(III)-contaminated water and sediments, and a non-flooded control soil were analysed for microbial biomass, total and active fungal mycelium, enzyme activities (i.e., FDA hydrolase, dehydrogenase, beta-glucosidase, urease, arylsulphatase, acid phosphatase) and bacterial diversity (DGGE characterisation). Biological and biochemical data were related with both total and selected fractions of Cr and Cu (the latter deriving from agricultural chemical products) as well as with total and extractable organic C. The growth and activity of soil microbial community were influenced by soil organic C content rather than Cu or Cr contents. In fact, positive correlations between all studied parameters and organic C content were found. On the contrary, negative correlations were observed only between total fungal mycelium, dehydrogenase, arylsulphatase and acid phosphatase activities and only one Cr fraction (the soluble, exchangeable and carbonate bound). However, total Cr content negatively affected the eubacterial diversity but it did not determine changes in soil activity, probably because of the redundancy of functions within species of soil microbial community. On the other hand, expressing biological and biochemical parameters per unit of total organic C, Cu pollution negatively influenced microbial biomass, fungal mycelium and several enzyme activities, confirming soil organic matter is able to mask the negative effects of Cu on microbial community.

Bacteria↗
PubMed2006

Root controls on soil microbial community structure in forest soils.

We assessed microbial community composition as a function of altered above- and belowground inputs to soil in forest ecosystems of Oregon, Pennsylvania, and Hungary as part of a larger Detritus Input and Removal Treatment (DIRT) experiment. DIRT plots, which include root trenching, aboveground litter exclusion, and doubling of litter inputs, have been established in forested ecosystems in the US and Europe that vary with respect to dominant tree species, soil C content, N deposition rate, and soil type. This study used phospholipid fatty-acid (PLFA) analysis to examine changes in the soil microbial community size and composition in the mineral soil (0-10 cm) as a result of the DIRT treatments. At all sites, the PLFA profiles from the plots without roots were significantly different from all other treatments. PLFA analysis showed that the rootless plots generally contained larger quantities of actinomycete biomarkers and lower amounts of fungal biomarkers. At one of the sites in an old-growth coniferous forest, seasonal changes in PLFA profiles were also examined. Seasonal differences in soil microbial community composition were greater than treatment differences. Throughout the year, treatments without roots continued to have a different microbial community composition than the treatments with roots, although the specific PLFA biomarkers responsible for these differences varied by season. These data provide direct evidence that root C inputs exert a large control on microbial community composition in the three forested ecosystems studied.

Plant Roots↗
PubMed1994

Microbial endoglycosidases for analyses of oligosaccharide chains in glycoproteins.

Microbial endoglycosidases are useful for elucidating the structure and function of the oligosaccharide chains of glycoconjugates. Most of the microbial endo-beta-N-acetylglucosaminidases including Endo-H can preferentially act on high-mannose type chains of asparagine-linked oligosaccharides of various glycoproteins. Among them, Flavobacterium sp. enzyme is produced in large amounts by the inducing cultivation. Using this enzyme, the role of oligosaccharide chains in various microbial glycoenzymes such as Rhizopus glucoamylase, and yeast invertase was examined. The findings suggested that the oligosaccharide chains of them are essential participants in the stabilization of the enzyme and in the protection from proteolytic inactivation. Novel endo-beta-N-acetylglucosaminidases were also found in the culture broths of microorganisms. Unlike most microbial endo-beta-N-acetylglucosaminidases, Endo-M of Mucor hiemalis could act on a complex type oligosaccharide chains, which is similar to Endo-F2 in multiple form of Endo-F from Flavobacterium meningosepticum. The complete amino acid sequences of Endo-F1, -F2, -F3, -H, and Flavobacterium sp. enzyme were determined. All of them had two highly conserved regions common to a number of chitinases. Endo-alpha-N-acetylgalactosaminidase which hydrolyzes the O-glycosidic linkages in glycoproteins was found in the culture broth of only a few microorganisms. The production of Alcaligenes sp. enzyme was highly induced by the addition of porcine gastric mucin in the culture medium. There is some evidence that endo-alpha-N-acetylgalactosaminidases may recognize not only the glycon but also the aglycon amino acids.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed2006

Community genomics among stratified microbial assemblages in the ocean's interior.

Microbial life predominates in the ocean, yet little is known about its genomic variability, especially along the depth continuum. We report here genomic analyses of planktonic microbial communities in the North Pacific Subtropical Gyre, from the ocean's surface to near-sea floor depths. Sequence variation in microbial community genes reflected vertical zonation of taxonomic groups, functional gene repertoires, and metabolic potential. The distributional patterns of microbial genes suggested depth-variable community trends in carbon and energy metabolism, attachment and motility, gene mobility, and host-viral interactions. Comparative genomic analyses of stratified microbial communities have the potential to provide significant insight into higher-order community organization and dynamics.

Amino Acid Sequence↗
PubMed2000

Prebiotics and probiotics: are they functional foods?

A probiotic is a viable microbial dietary supplement that beneficially affects the host through its effects in the intestinal tract. Probiotics are widely used to prepare fermented dairy products such as yogurt or freeze-dried cultures. In the future, they may also be found in fermented vegetables and meats. Several health-related effects associated with the intake of probiotics, including alleviation of lactose intolerance and immune enhancement, have been reported in human studies. Some evidence suggests a role for probiotics in reducing the risk of rotavirus-induced diarrhea and colon cancer. Prebiotics are nondigestible food ingredients that benefit the host by selectively stimulating the growth or activity of one or a limited number of bacteria in the colon. Work with prebiotics has been limited, and only studies involving the inulin-type fructans have generated sufficient data for thorough evaluation regarding their possible use as functional food ingredients. At present, claims about reduction of disease risk are only tentative and further research is needed. Among the claims are constipation relief, suppression of diarrhea, and reduction of the risks of osteoporosis, atherosclerotic cardiovascular disease associated with dyslipidemia and insulin resistance, obesity, and possibly type 2 diabetes. The combination of probiotics and prebiotics in a synbiotic has not been studied. This combination might improve the survival of the bacteria crossing the upper part of the gastrointestinal tract, thereby enhancing their effects in the large bowel. In addition, their effects might be additive or even synergistic.

Bifidobacterium↗
PubMed2004

Microbes and their products--physiological effects upon mammalian mucosa.

A dynamic array of interactions occurs between pathogens and host mucosal surfaces. The signature molecules unique to microbial pathogens allow the mammalian immune system to recognize them as non-self. This recognition, mediated by the toll-like receptor proteins, results in innate immune responses targeted against the invading organism. Pathogens also elaborate a variety of proteins that actively engage host signaling pathways and subvert them to facilitate their growth and dispersal. These interactions, developed over a long evolutionary period, have been specialized to exquisite detail. These proteins and toxins are either secreted into the medium or directly delivered into host cells by specialized secretion systems. An array of host function alterations is mediated by microbial pathogens including inflammatory responses, secretory responses, alteration of host cytoskeleton, disruption of epithelial tight junctions and apoptosis. The signaling axes involved in these interactions are potential targets for therapeutic strategies against infectious microbes.

Animals↗
PubMed1989

Pentoxifylline modulation of plasma membrane functions in human polymorphonuclear leukocytes.

Pentoxifylline is known to have major effects on cell membrane function in mammalian cells, including human leukocytes. The protective effects of this agent in animal models of infection and inflammation may be due to alterations in phagocyte (neutrophil and macrophage) function. However, the exact mechanism of action of pentoxifylline is unknown. In this study, we evaluated the effect of the drug on several membrane-associated activities in human polymorphonuclear neutrophils and investigated possible mechanisms for the observed changes in neutrophil function. Pentoxifylline inhibited ingestion of microbial particles (Staphylococcus aureus and zymosan); decreased superoxide generation activated by zymosan, formyl-methionyl-leucyl-phenylalanine, and concanavalin A (but not phorbol myristate acetate); and decreased uptake (transport) of adenosine stimulated by formyl-methionyl-leucyl-phenylalanine and zymosan. In contrast, pentoxifylline actually increased clindamycin uptake in zymosan-stimulated polymorphonuclear neutrophils. However, pentoxifylline had no effect on uptake of adenosine or clindamycin in unstimulated neutrophils. In comparison with known inhibitors of nucleoside transport (nitrobenzylthioinosine and dipyridamole), the results suggested that pentoxifylline does not bind to membrane nucleoside transport receptors. At concentrations which inhibit neutrophil function, pentoxifylline activity is not mediated through external membrane nucleoside regulatory sites. Thus, pentoxifylline affects the activation signal chain at a point beyond the membrane receptors. Whatever its precise mechanism of action, pentoxifylline has a striking modulatory effect on cell membrane-associated responses in stimulated leukocytes and may prove useful for control of injurious inflammatory states.

Adenosine↗
PubMed2001

On the species of origin: diagnosing the source of symbiotic transcripts.

BACKGROUND: Most organisms have developed ways to recognize and interact with other species. Symbiotic interactions range from pathogenic to mutualistic. Some molecular mechanisms of interspecific interaction are well understood, but many remain to be discovered. Expressed sequence tags (ESTs) from cultures of interacting symbionts can help identify transcripts that regulate symbiosis, but present a unique challenge for functional analysis. Given a sequence expressed in an interaction between two symbionts, the challenge is to determine from which organism the transcript originated. For high-throughput sequencing from interaction cultures, a reliable computational approach is needed. Previous investigations into GC nucleotide content and comparative similarity searching provide provisional solutions, but a comparative lexical analysis, which uses a likelihood-ratio test of hexamer counts, is more powerful. RESULTS: Validation with genes whose origin and function are known yielded 94% accuracy. Microbial (non-plant) transcripts comprised 75% of a Phytophthora sojae-infected soybean (Glycine max cv Harasoy) library, contrasted with 15% or less in root tissue libraries of Medicago truncatula from axenic, Phytophthora medicaginis-infected, mycorrhizal, and rhizobacterial treatments. Mycorrhizal libraries contained about 23% microbial transcripts; an axenic plant library contained a similar proportion of putative microbial transcripts. CONCLUSIONS: Comparative lexical analysis offers numerous advantages over alternative approaches. Many of the transcripts isolated from mixed cultures were of unknown function, suggesting specificity to symbiotic metabolism and therefore candidates likely to be interesting for further functional investigation. Future investigations will determine whether the abundance of non-plant transcripts in a pure plant library indicates procedural artifacts, horizontally transferred genes, or other phenomena.

Computational Biology↗
PubMed1999

Phagocytic antigen processing and effects of microbial products on antigen processing and T-cell responses.

Processing of exogenous antigens and microbes involves contributions by multiple different endocytic and phagocytic compartments. During the processing of soluble antigens, different endocytic compartments have been demonstrated to use distinct antigen-processing mechanisms and to process distinct sets of antigenic epitopes. Processing of particulate and microbial antigens involves phagocytosis and functions contributed by phagocytic compartments. Recent data from our laboratory demonstrate that phagosomes containing antigen-conjugated latex beads are fully competent class II MHC (MHC-II) antigen-processing organelles, which generate peptide:MHC-II complexes. In addition, phagocytosed antigen enters an alternate class I MHC (MHC-I) processing pathway that results in loading of peptides derived from exogenous antigens onto MHC-I molecules, in contrast to the cytosolic antigen source utilized by the conventional MHC-I antigen-processing pathway. Antigen processing and other immune response mechanisms may be activated or inhibited by microbial components to the benefit of either the host or the pathogen. For example, antigen processing and T-cell responses (e.g. Th1 vs Th2 differentiation) are modulated by multiple distinct microbial components, including lipopolysaccharide, cholera toxin, heat labile enterotoxin of Escherichia coli, DNA containing CpG motifs (found in prokaryotic and invertebrate DNA but not mammalian DNA) and components of Mycobacterium tuberculosis.

Animals↗
PubMed2005

Identification of bacteria potentially responsible for oxic and anoxic sulfide oxidation in biofilters of a recirculating mariculture system.

Bacteria presumably involved in oxygen- or nitrate-dependent sulfide oxidation in the biofilters of a recirculating marine aquaculture system were identified using a new application of reverse transcription-PCR denaturing gradient gel electrophoresis (DGGE) analysis termed differential-transcription (DT)-DGGE. Biofilter samples were incubated in various concentrations of sulfide or thiosulfate (0 to 5 mM) with either oxygen or nitrate as the sole electron acceptor. Before and after short-term incubations (10 to 20 h), total DNA and RNA were extracted, and a 550-bp fragment of the 16S rRNA genes was PCR amplified either directly or after reverse transcription. DGGE analysis of DNA showed no significant change of the original microbial consortia upon incubation. In contrast, DGGE of cDNA revealed several phylotypes whose relative band intensities markedly increased or decreased in response to certain incubation conditions, indicating enhanced or suppressed rRNA transcription and thus implying metabolic activity under these conditions. Specifically, species of the gammaproteobacterial genus Thiomicrospira and phylotypes related to symbiotic sulfide oxidizers could be linked to oxygen-dependent sulfide oxidation, while members of the Rhodobacteraceae (genera Roseobacter, Rhodobacter, and Rhodobium) were putatively active in anoxic, nitrate-dependent sulfide oxidation. For all these organisms, the physiology of their closest cultured relatives matches their DT-DGGE-inferred function. In addition, higher band intensities following exposure to 5 mM sulfide and nitrate were observed for Thauera-, Hydrogenophaga-, and Dethiosulfovibrio-like phylotypes. For these genera, nitrate-dependent sulfide oxidation has not been documented previously and therefore DT-DGGE might indicate a higher relative tolerance to high sulfide concentrations than that of other community members. We anticipate that DT-DGGE will be of general use in tracing functionally equivalent yet phylogenetically diverse microbial populations in nature.

Aquaculture↗
PubMed1979

Nonspecific immune determinants in the patient with unresectable gastrointestinal carcinoma.

Assays of immune function (recall skin tests to microbial antigens; total circulating lymphocytes, T-cells, B-cells; lymphocyte blastogenesis with PHA, Con A, and pokeweed mitogens; and serum immunoglobulins IgA, IgM, IgG) were obtained in 408 patients with unresectable gastrointestinal carcinoma. The overall patient population, in comparison to normal controls, was characterized by reduced response to recall skin tests, reduced total lymphocyte and T-cell counts, reduced lymphocyte blastogenesis assays, increased B-cell counts and increased IgA and IgM. Significant immunosuppression was associated with prior radiation or chemotherapy, and with impaired patient performance status. There was no apparent correlation between extent of clinically evident malignant disease and immune function within this patient population. No assay of immune function matched the prognostic value of the more readily available and less expensive determinations of performance status, serum alkaline phosphatase, or SGOT. Only reactivity to recall skin tests had a significant correlation to patient survival independent of performance status. Among patients with little or no disability, only intensity of skin test reactivity correlated significantly with survival; and among those with greater disability, there was correlation only with proportion of skin tests positive. The combination of candida and streptokinase antigens provided the best recall skin test survival correlation. Adding a third, fourth, or fifth antigen did not add to prognostic value. From an overall standpoint, the immune determinants which we studied do not appear to provide useful additions to the evaluation of the patient with unresectable gastrointestinal cancer.

Age Factors↗
PubMed2025

Pangenome analysis of Lactobacillus mulieris strains reveals distinct subspecies clusters with defined ecological adaptations.

Lactobacillus mulieris is a recently described species, reportedly isolated from human urine, vagina, and gut. Previous genomic studies of L. mulieris highlighted significant genetic diversity among its strains. To gain a deeper understanding of this genomic diversity, we conducted a comprehensive genomic comparison of 70 L. mulieris strains from diverse sources. Phylogenomic and genome relatedness analysis identified three distinct clades, each representing a potential subspecies cluster. Pangenome analysis revealed distinct gene clusters shaping the functional characteristics and unique ecological adaptations of each clade. Clade 1 demonstrated a generalist lifestyle, with strains isolated from diverse sources and enriched in serine/threonine protein kinases, suggesting adaptive versatility. Clade 2, predominantly composed of urinary isolates, displayed enrichment in genes facilitating nutrient acquisition and osmotic regulation, enabling survival in the nutrient-limited and high osmolarity conditions of the urinary tract. Clade 3, exclusively composed of vaginal isolates, exhibited significant enrichment in genes supporting glycogen metabolism, carbohydrate transport, and capsular polysaccharide biosynthesis-features indicative of adaptation to the vaginal environment. Collectively, our findings provide essential genomic insights into the ecological specialization of L. mulieris, shedding light on their genetic variability and adaptive traits within their respective ecological niches.IMPORTANCERecognizing the genomic diversity within Lactobacillus mulieris is essential for understanding its ecological specialization and adaptation strategies across distinct human-associated environments. By identifying three distinct clades with unique functional traits, our study highlights the critical role of niche-specific genetic adaptations in microbial survival. The presence of specialized gene functions within each clade underscores how evolutionary pressures shape bacterial resilience in different environments. Despite their coexistence in overlapping environments, these clades exhibit distinct genomic profiles that may influence their colonization potential and interactions with the host and within the host-associated microbiota. Our findings emphasize the need for a classification framework that accounts for these genetic and functional differences and the necessity for further investigation to understand their distinct roles and impact on human health.

Humans↗
PubMed1994

TNF-alpha and IL-6 expression in perfused rat liver after intraportal candidemia vs. E. coli or S. aureus bacteremia.

We tested the hypothesis that regulation of tumor necrosis factor-alpha (TNF-alpha) and IL-6 by the liver differs after intraportal challenge with Candida albicans spp. vs. gram-negative or gram-positive bacteria, independent of microbial clearance kinetics or hepatic O2 consumption (VO2). Buffer-perfused rat livers were infected with equivalent inocula (10(9) colony-forming units) of viable Escherichia coli serotype 055:B5 (EC), exotoxin C-producing Staphylococcus aureus (SA), or two strains of yeast phase C. albicans (CA-1 and CA-2). Microbial clearance and circulating cytokine levels were assessed over 180 min while monitoring VO2 and functional parameters, after which organ-based microbial killing, cell-associated TNF-alpha, and cytokine mRNA levels were determined. Compared with saline controls (normal saline solution; NSS), circulating and cell-associated TNF-alpha and TNF-alpha transcripts minimally increased after CA. In contrast, large increases in perfusate TNF-alpha occurred after EC, peaking at 180 min [135 +/- 32 U/ml (mean + SE)], concomitant with rises in cell-associated cytokine and TNF-alpha transcripts (P < 0.01 vs. NSS). Circulating TNF-alpha also rose after SA but neither cell-associated nor mRNA levels exceeded NSS values. There were no pathogen-specific differences in microbial clearance or VO2. IL-6 gene expression paralleled that for TNF-alpha, but IL-6 bioactivity in perfusates was inhibited by TNF-alpha-dependent and -independent mechanisms. We conclude that hepatic TNF-alpha and IL-6 expression are differentially regulated after taxonomically diverse microbial challenges, with E. coli eliciting the strongest and Candida spp. the weakest stimulatory responses.

Animals↗
PubMed2003

Microbial community utilization of recalcitrant and simple carbon compounds: impact of oak-woodland plant communities.

Little is known about how the structure of microbial communities impacts carbon cycling or how soil microbial community composition mediates plant effects on C-decomposition processes. We examined the degradation of four (13)C-labeled compounds (starch, xylose, vanillin, and pine litter), quantified rates of associated enzyme activities, and identified microbial groups utilizing the (13)C-labeled substrates in soils under oaks and in adjacent open grasslands. By quantifying increases in non-(13)C-labeled carbon in microbial biomarkers, we were also able to identify functional groups responsible for the metabolism of indigenous soil organic matter. Although microbial community composition differed between oak and grassland soils, the microbial groups responsible for starch, xylose, and vanillin degradation, as defined by (13)C-PLFA, did not differ significantly between oak and grassland soils. Microbial groups responsible for pine litter and SOM-C degradation did differ between the two soils. Enhanced degradation of SOM resulting from substrate addition (priming) was greater in grassland soils, particularly in response to pine litter addition; under these conditions, fungal and Gram+ biomarkers showed more incorporation of SOM-C than did Gram- biomarkers. In contrast, the oak soil microbial community primarily incorporated C from the added substrates. More (13)C (from both simple and recalcitrant sources) was incorporated into the Gram- biomarkers than Gram+ biomarkers despite the fact that the Gram+ group generally comprised a greater portion of the bacterial biomass than did markers for the Gram- group. These experiments begin to identify components of the soil microbial community responsible for decomposition of different types of C-substrates. The results demonstrate that the presence of distinctly different plant communities did not alter the microbial community profile responsible for decomposition of relatively labile C-substrates but did alter the profiles of microbial communities responsible for decomposition of the more recalcitrant substrates, pine litter and indigenous soil organic matter.

Benzaldehydes↗
PubMed2025

Biophysical metabolic modeling of complex bacterial colony morphology.

Microbial colony growth is shaped by the physics of biomass propagation and nutrient diffusion and by the metabolic reactions that organisms activate as a function of the surrounding environment. While microbial colonies have been explored using minimal models of growth and motility, full integration of biomass propagation and metabolism is still lacking. Here, building upon our framework for computation of microbial ecosystems in time and space (COMETS), we combine dynamic flux balance modeling of metabolism with collective biomass propagation and demographic fluctuations to provide nuanced simulations of E. coli colonies. Simulations produced realistic colony morphology, consistent with our experiments. They characterize the transition between smooth and furcated colonies and the decay of genetic diversity. Furthermore, we demonstrate that under certain conditions, biomass can accumulate along "metabolic rings" that are reminiscent of coffee-stain rings but have a completely different origin. Our approach is a key step toward predictive microbial ecosystems modeling. A record of this paper's transparent peer review process is included in the supplemental information.

Models, Biological↗
PubMedDate not supplied

Molecular microbial biodiversity assessment: a biological indicator of soil health.

The soil performs a variety of key functions: (i) provides the food, fuel, and fiber needs of the world's population, (ii) regulates the quality of the air and water, (iii) decomposes organic wastes, (iv) recycles nutrients, and (v) acts as a sink for pollutants (including global gases). Soil degradation is increasingly recognized as an urgent environmental issue and a crucial need exists for the capacity to evaluate soil health. After all, soil health is a key component in sustaining the different world's ecosystems and the myriad of natural and socioeconomic systems they support. In this respect, soil health has been defined as the "continued capacity of a specific kind of soil to function as a vital living system, within natural or managed ecosystem boundaries, to sustain plant and animal productivity, to maintain or enhance the quality of air and water environments, and to support human health and habitation". A biological indicator is an organism, a part of an organism, or a community of organisms, used to obtain information about environmental quality. The assessment of microbial biodiversity has the potential to provide useful insight into the health and functioning of soil. Our inability to culture most microorganisms that are present in soils has, until recently, impaired studying the relationships between the structure and the function of soil microbial communities. This shortcoming has been recently overcome by using several molecular techniques that allow the detection, enumeration, and characterization of soil microorganisms without cultivation.

Bacteria↗