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The current study proposes RBBR biosorption by Clostridium beijerinckii DSMZ 6422 biomass remaining after biobutanol production from pumpkin peel (PP) by a zero-waste approach . Efficient biobutanol production was achieved by investigating initial PP concentrations (5–20% without or with enzymatic hydrolysis) and fermentation time. According to this, the highest concentrations of biobutanol and total ABE were obtained as 4.87 g/L and 8.13 g/L in the presence of 10% PP without enzymatic hydrolysis at 96 h. Furthermore, based on the zero-waste approach, C. beijerinckii DSMZ 6422 biomass obtained after biofuel production was used as a biosorbent for the removal of RBBR dye. Response surface methodology (RSM), commonly utilized for the experimental design, was used to specify the optimized biosorption conditions of RBBR, including initial dye concentration (50–200 mg/L), initial pH (2–6), biosorbent concentration (1–3 g/L), and contact time (0–240 min). The highest biosorption under optimized conditions with RSM was 98% in the presence of 194.36 mg/L RBBR and 2.65 g/L biosorbent at pH 2 and 15 min. This is the first report in the literature about the biosorption of RBBR dye by anaerobic C. beijerinckii biomass after the biobutanol production process. This study also shows the efficient usage of agricultural and microbial wastes in different areas based on zero-waste applications.

* AOA and comammox bacteria can be more abundant and active than AOB/NOB at WWTPs. * Coupled DNRA/anammox and NO x -DAMO/anammox/comammox processes are demonstrated. * Substrate level, SRT and stressors determine the niches of overlooked microbes. * Applications of overlooked microbes in enhancing nitrogen removal are promising. Nitrogen-cycling microorganisms play key roles at the intersection of microbiology and wastewater engineering. In addition to the well-studied ammonia oxidizing bacteria, nitrite oxidizing bacteria, heterotrophic denitrifiers, and anammox bacteria, there are some other N-cycling microorganisms that are less abundant but functionally important in wastewater nitrogen removal. These microbes include, but not limited to ammonia oxidizing archaea (AOA), complete ammonia oxidation (comammox) bacteria, dissimilatory nitrate reduction to ammonia (DNRA) bacteria, and nitrate/nitrite-dependent anaerobic methane oxidizing (NO x -DAMO) microorganisms. In the past decade, the development of high-throughput molecular technologies has enabled the detection, quantification, and characterization of these minor populations. The aim of this review is therefore to synthesize the current knowledge on the distribution, ecological niche, and kinetic properties of these \"overlooked\" N-cycling microbes at wastewater treatment plants. Their potential applications in novel wastewater nitrogen removal processes are also discussed. A comprehensive understanding of these overlooked N-cycling microbes from microbiology, ecology, and engineering perspectives will facilitate the design and operation of more efficient and sustainable biological nitrogen removal processes.

The quality of feed, including its microbiological characteristics, is important for the organization of full-value feeding of animals in agriculture. So, the means of non-reagent processing of feeds, including cavitation treatment, are becoming more widespread. In our study, it was shown that the amount of mesophilic aerobic and facultative anaerobic microorganisms (QMAFAnM) decreases after a 5-min treatment of the test samples (chalk, fuz, bran, and zeolite) (1.1–35 times) compared to untreated samples, while an increase in the duration of exposure is proportional to the expression of the bactericidal effect. A study of the bioluminescent response of the test strain Escherichia coli K12 TG1 under the influence of the test samples showed inhibition of bioluminescence under the action of chalk and an increase in luminescence during incubation with fusa and bran. When examining the growth rates of strains E. Coli 675 and Bifidobacterium longum B379M , it was found that water and zeolite treated with cavitation suppressed the growth of E. coli 675 , while the growth of Bifidobacterium longum B379M was higher than the control values at the end of the experiment. So, cavitation processing can cause the death of microflora of feed additives, at the same time, as a result of the dissociation of a complex of organic polymers, contributing to the positive response of probiotic strains. These studies can be used in agriculture in the preparation of feed additives from waste from the processing industry.

The ocean is home to a diverse and metabolically versatile microbial community that performs the complex biochemical transformations that drive the nitrogen cycle, including nitrogen fixation, assimilation, nitrification and nitrogen loss processes. In this Review, we discuss the wealth of new ocean nitrogen cycle research in disciplines from metaproteomics to global biogeochemical modelling and in environments from productive estuaries to the abyssal deep sea. Influential recent discoveries include new microbial functional groups, novel metabolic pathways, original conceptual perspectives and ground-breaking analytical capabilities. These emerging research directions are already contributing to urgent efforts to address the primary challenge facing marine microbiologists today: the unprecedented onslaught of anthropogenic environmental change on marine ecosystems. Ocean warming, acidification, nutrient enrichment and seawater stratification have major effects on the microbial nitrogen cycle, but widespread ocean deoxygenation is perhaps the most consequential for the microorganisms involved in both aerobic and anaerobic nitrogen transformation pathways. In turn, these changes feed back to the global cycles of greenhouse gases such as carbon dioxide and nitrous oxide. At a time when our species casts a lengthening shadow across all marine ecosystems, timely new advances offer us unique opportunities to understand and better predict human impacts on nitrogen biogeochemistry in the changing ocean of the Anthropocene.The ocean is home to a diverse and metabolically versatile microbial community that performs the complex biochemical transformations that drive the nitrogen cycle. In this Review, Hutchins and Capone explore the latest developments in our understanding of the role of microorganisms in the marine nitrogen cycle, including new taxa, pathways, methods and concepts. They also discuss opportunities to understand and better predict the effects of humans and global change.

The skin barrier protects the human body from invasion by exogenous and pathogenic microorganisms. A breach in this barrier exposes the underlying tissue to microbial contamination, which can lead to infection, delayed healing, and further loss of tissue and organ integrity. Delayed wound healing and chronic wounds are associated with comorbidities, including diabetes, advanced age, immunosuppression and autoimmune disease. The wound microbiota can influence each stage of the multi-factorial repair process and influence the likelihood of an infection. Pathogens that commonly infect wounds, such as Staphylococcus aureus and Pseudomonas aeruginosa, express specialized virulence factors that facilitate adherence and invasion. Biofilm formation and other polymicrobial interactions contribute to host immunity evasion and resistance to antimicrobial therapies. Anaerobic organisms, fungal and viral pathogens, and emerging drug-resistant microorganisms present unique challenges for diagnosis and therapy. In this Review, we explore the current understanding of how microorganisms present in wounds impact the process of skin repair and lead to infection through their actions on the host and the other microbial wound inhabitants.In this Review, Uberoi, McCready-Vangi and Grice explore the diversity of microorganisms present in wounds and examine the mechanisms through which they invade skin tissues, impair skin repair and cause infection.

The gut microbiota affects human health, but we are only just beginning to develop a mechanistic understanding of some of the host-microbe interactions involved. Litvak et al. review how host colon epithelial cells mediate the symbiosis. Healthy colonocytes maintain anaerobic conditions in the gut lumen because their metabolism ensures rapid oxygen consumption. Such conditions select for obligate anaerobic organisms. These tend to be those that consume dietary fiber and produce short-chain fatty acids beneficial to the host. If there is a shift in colonocyte metabolism—because of disease, diet, or other damage—the epithelium becomes oxygenated. The presence of oxygen allows expansion of facultative aerobic organisms. Microbes in genera that include pathogens are often oxygen-tolerant, and dysbiosis can be the result. Science , this issue p. eaat9076 An imbalance in the colonic microbiota might underlie many human diseases, but the mechanisms that maintain homeostasis remain elusive. Recent insights suggest that colonocyte metabolism functions as a control switch, mediating a shift between homeostatic and dysbiotic communities. During homeostasis, colonocyte metabolism is directed toward oxidative phosphorylation, resulting in high epithelial oxygen consumption. The consequent epithelial hypoxia helps to maintain a microbial community dominated by obligate anaerobic bacteria, which provide benefit by converting fiber into fermentation products absorbed by the host. Conditions that alter the metabolism of the colonic epithelium increase epithelial oxygenation, thereby driving an expansion of facultative anaerobic bacteria, a hallmark of dysbiosis in the colon. Enteric pathogens subvert colonocyte metabolism to escape niche protection conferred by the gut microbiota. The reverse strategy, a metabolic reprogramming to restore colonocyte hypoxia, represents a promising new therapeutic approach for rebalancing the colonic microbiota in a broad spectrum of human diseases.

Soils represent the largest carbon reservoir within terrestrial ecosystems. The mechanisms controlling the amount of carbon stored and its feedback to the climate system, however, remain poorly resolved. Global carbon models assume that carbon cycling in upland soils is entirely driven by aerobic respiration; the impact of anaerobic microsites prevalent even within well-drained soils is missed within this conception. Here, we show that anaerobic microsites are important regulators of soil carbon persistence, shifting microbial metabolism to less efficient anaerobic respiration, and selectively protecting otherwise bioavailable, reduced organic compounds such as lipids and waxes from decomposition. Further, shifting from anaerobic to aerobic conditions leads to a 10-fold increase in volume-specific mineralization rate, illustrating the sensitivity of anaerobically protected carbon to disturbance. The vulnerability of anaerobically protected carbon to future climate or land use change thus constitutes a yet unrecognized soil carbon–climate feedback that should be incorporated into terrestrial ecosystem models. Mechanisms controlling soil carbon storage and feedbacks to the climate system remain poorly constrained. Here, the authors show that anaerobic microsites stabilize soil carbon by shifting microbial metabolism to less efficient anaerobic respiration and protecting reduced organic compounds from decomposition.

Polyaromatic hydrocarbons (PAHs) are considered as hazardous organic priority pollutants. PAHs have immense public concern and critical environmental challenge around the globe due to their toxic, carcinogenic, and mutagenic properties, and their ubiquitous distribution, recalcitrance as well as persistence in environment. The knowledge about harmful effects of PAHs on ecosystem along with human health has resulted in an interest of researchers on degradation of these compounds. Whereas physico-chemical treatment of PAHs is cost and energy prohibitive, bioremediation i.e. degradation of PAHs using microbes is becoming an efficient and sustainable approach. Broad range of microbes including bacteria, fungi, and algae have been found to have capability to use PAHs as carbon and energy source under both aerobic and anaerobic conditions resulting in their transformation/degradation. Microbial genetic makeup containing genes encoding catabolic enzymes is responsible for PAH-degradation mechanism. The degradation capacity of microbes may be induced by exposing them to higher PAH-concentration, resulting in genetic adaptation or changes responsible for high efficiency towards removal/degradation. In last few decades, mechanism of PAH-biodegradation, catabolic gene system encoding catabolic enzymes, and genetic adaptation and regulation have been investigated in detail. This review is an attempt to overview current knowledge of microbial degradation mechanism of PAHs, its genetic regulation with application of genetic engineering to construct genetically engineered microorganisms, specific catabolic enzyme activity, and application of bioremediation for reclamation of PAH-contaminated sites. In addition, advanced molecular techniques i.e. genomic, proteomic, and metabolomic techniques are also discussed as powerful tools for elucidation of PAH-biodegradation/biotransformation mechanism in an environmental matrix.

Lignin, the most abundant renewable aromatic compound in nature, is an excellent feedstock for value-added bioproducts manufacturing; while the intrinsic heterogeneity and recalcitrance of which hindered the efficient lignin biorefinery and utilization. Compared with chemical processing, bioprocessing with microbial and enzymatic catalysis is a clean and efficient method for lignin depolymerization and conversion. Generally, lignin bioprocessing involves lignin decomposition to lignin-based aromatics via extracellular microbial enzymes and further converted to value-added bioproducts through microbial metabolism. In the review, the most recent advances in degradation and conversion of lignin to value-added bioproducts catalyzed by microbes and enzymes were summarized. The lignin-degrading microorganisms of white-rot fungi, brown-rot fungi, soft-rot fungi, and bacteria under aerobic and anaerobic conditions were comparatively analyzed. The catalytic metabolism of the microbial lignin-degrading enzymes of laccase, lignin peroxidase, manganese peroxidase, biphenyl bond cleavage enzyme, versatile peroxidase, and β-etherize was discussed. The microbial metabolic process of H-lignin, G-lignin, S-lignin based derivatives, protocatechuic acid, and catechol was reviewed. Lignin was depolymerized to lignin-derived aromatic compounds by the secreted enzymes of fungi and bacteria, and the aromatics were converted to value-added compounds through microbial catalysis and metabolic engineering. The review also proposes new insights for future work to overcome the recalcitrance of lignin and convert it to value-added bioproducts by microbial and enzymatic catalysis.

Microbial food spoilage is a major contributor to food waste and, hence, to the negative environmental sustainability impacts of food production and processing. Globally, it is estimated that 15–20% of food is wasted, with waste, by definition, occurring after primary production and harvesting (for example, in households and food service establishments). Although the causative agents of food spoilage are diverse, many microorganisms are major contributors across different types of foods. For example, the genus Pseudomonas causes spoilage in various raw and ready-to-eat foods. Aerobic sporeformers (for example, members of the genera Bacillus, Paenibacillus and Alicyclobacillus) cause spoilage across various foods and beverages, whereas anaerobic sporeformers (for example, Clostridiales) cause spoilage in a range of products that present low-oxygen environments. Fungi are also important spoilage microorganisms, including in products that are not susceptible to bacterial spoilage due to their low water activity or low pH. Strategies that can reduce spoilage include improved control of spoilage microorganisms in raw material and environmental sources as well as application of microbicidal or microbiostatic strategies (for example, to products and packaging). Emerging tools (for example, systems models and improved genomic tools) represent an opportunity for rational design of systems, processes and products that minimize microbial food spoilage.In this Review, Snyder et al. discuss the global impacts of food spoilage, mechanisms and causative agents, and strategies and emerging tools to control microbial food spoilage.