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Soil properties, the chemical composition of cementation solution, injection technique, and environmental conditions have all been extensively studied as variables influencing microbially induced carbonate precipitation performance. However, despite the fact that different researchers have used different bacterial suspensions, the influence of bacterial suspension type, more specifically some organic matters in bacterial suspensions, which can play a key role in the morphology and mechanical properties of CaC[O.sub.3], has often been overlooked. In this study, the harvested bacterial solutions were centrifuged to separate bacterial cells and supernatant. The precipitated cells were then diluted with three distinct solutions: supernatant (RB), fresh culture medium (FB), and 0.9% NaCl solution (NB), which were subsequently utilized to stabilize the sand. The results indicated that the bacterial suspension type could greatly impact the strength of biocemented sand, particularly coarse and medium sand. Differences in unconfined compressive strength can be related to differences in precipitated CaC[O.sub.3] microstructures, morphologies, and compositions, which were examined using scanning electron microscopy, X-ray diffraction analysis, and Fourier transform infrared spectroscopy. Key words: microbially induced calcite precipitation (MICP), unconfined compressive strength (UCS), bacterial suspension type, microstructure Les proprietes du sol, la composition chimique de la solution de cimentation, la technique d'injection et les conditions environnementales ont toutes ete largement etudiees comme variables influencant les performances du MICP. Cependant, malgre le fait que differents chercheurs aient utilise differentes suspensions bacteriennes, l'influence du type de suspension bacterienne, plus precisement de certaines matieres organiques dans les suspensions bacteriennes, qui peuvent jouer un role cle dans la morphologie et les proprietes mecaniques du CaC[O.sub.3], a souvent ete negligee. Dans cette etude, les solutions bacteriennes recoltees ont ete centrifugees pour separer les cellules bacteriennes et le surnageant. Les cellules precipitees ont ensuite ete diluees dans trois solutions distinctes : surnageant (RB), milieu de culture frais (FB) et solution de NaCl a 0,9% (NB), qui ont ensuite ete utilises pour stabiliser le sable. Les resultats ont indique que le type de suspension bacterienne pouvait avoir un impact important sur la resistance du sable biocimente, en particulier le sable grossier et moyen. Les differences de NGC peuvent etre liees aux differences de microstructures, de morphologies et de compositions du CaC[O.sub.3] precipite, qui ont ete examinees a l'aide de la microscopie electronique a balayage (MEB), de l'analyse par diffraction des rayons X (DRX) et de la spectroscopie infrarouge transformee de Fourier (IRTF). [Traduit par la Redaction] Mots-cles : precipitation de calcite induite par les microbes (MICP), resistance a la compression non confinee (UCS), type de suspension bacterienne, microstructure, Introduction The microbially induced carbonate precipitation (MICP)-based soil improvement approach has been introduced to geotechnical engineering for decades. Several studies have been conducted to investigate the performance of MICP in [...]

Soils provide the substrate for important microbial mechanisms that moderate a variety of processes in both managed and natural terrestrial ecosystems. Australian soils are particularly 'stressed' and are considered to be highly weathered and nutrient deficient. This places increased pressure on the Australian cotton industry to sustainably increase productivity to support the fibre demands of a growing global population. We explored Vertosol subsoils (>30 cm) under rotational cotton crops, measuring the distribution of soil microbial activity (SMA) and biomass (SMB) to 100 cm depth, as influenced by crop system and time, using respiration-based experiments. Seasonal SMA fluctuations were considered by capturing the long-term SMA between systems using stable oxygen isotope methodology. Our results indicate that subsoils contributed 47% of SMA, regardless of system, but subsoil SMB (26%) was constrained by resource availability. Long-term SMA was not significantly influenced by depth and system, presumably as a consequence of the shrink-swell nature of Vertosols facilitating organic matter movement down the profile. The impact of this organic matter on the activity of indigenous microorganisms below the top 30 cm of the profile highlights a need to consider deeper soil when unravelling the potential microbial benefits to our cropping systems. Additional keywords: agronomy, isotope techniques, soil microbiology, soil organic matter, Vertisol., Introduction The terrestrial biosphere is facing increasing pressures to meet the food and fibre demands of a growing world population (Fedoroff et al. 2010; Godfray el at. 2010). A prominent [...]

Genomics studies are helping to reveal how bacteria and archaea influence one of Earth's largest carbon stores as it begins to thaw. Genomics studies are helping to reveal how bacteria and archaea influence one of Earth's largest carbon stores as it begins to thaw., Author(s): Monique Brouillette Author Affiliations: A boardwalk for traversing Sweden's Stordalen Mire sinks in the thawing landscape. Credit: Moira Hough In a boggy landscape a line of boardwalk stretches into [...]

Coral reefs globally are increasingly impacted by climate change. High temperature and pCO.sub.2 levels disrupt multiple physiological and biochemical pathways in marine organisms, often leading to disease and mortality in sensitive reef species. Host-associated microbes contribute critical functions that underpin host health, and environmentally induced changes in microbial communities represent a potential source for new metabolic features within holobiont systems. However, whether the acquisition of new beneficial microbial functions contributes to environmental acclimatisation of reef species is currently unknown. Using extensively studied model systems, we identify potential direct and indirect microbiome-mediated mechanisms that may contribute to environmental acclimatisation in reef invertebrate species. These mechanisms include increasing energy metabolism in the host, reduction of oxidative stress, regulation of nutrients in host cells, and increased pathogen resistance. We also propose a robust experimental strategy to test how microbial metabolic pathways may facilitate environmental acclimatisation of reef taxa. Understanding the mechanisms of microbiome-mediated acclimatisation and the timescales over which it can occur will be critical for predicting reef ecosystem dynamics under future climate scenarios and applying effective reef conservation strategies., Author(s): Emma Marangon [sup.1] [sup.2] [sup.3] , Patrick W. Laffy [sup.1] [sup.3] , David G. Bourne [sup.1] [sup.2] [sup.3] , Nicole S. Webster [sup.1] [sup.3] [sup.4] Author Affiliations: (1) grid.1046.3, [...]

Increasing demands of groundwater in petroleum-recovering regions could elevate the level and mobility of arsenic in groundwater as a result of the enhanced dissolution of arsenic-bearing iron or manganese oxide due to the accelerated sulfate reduction by microorganisms in a reductive environment. To substantiate this possibility, groundwater samples were collected from 220 water wells in the nearby petroleum wells in Kuitun. Dissolved arsenic, iron, manganese, and sulfate levels and pH in groundwater samples were analyzed. The dissolved arsenic levels in groundwater varied from <2.3 to 789.4 μg·L−1, in which approximately 96.4% of the measured values exceeded the allowed limits of the World Health Organization. An inverse relation existed between dissolved arsenic and sulfate levels. Most of the high arsenic-level samples (>300 μg·L−1) were found in wells at close proximity to petroleum wells where a high iron or manganese level was also detected. The oil-exploring activity in the study region seemed to have enhanced the microbial reduction of sulfate in underground environment and hence the level of arsenic in groundwater. The microbial sulfate reduction coupled with the reduction of arsenic-bearing iron oxides in the groundwater environment may explain the spatial heterogeneity of the arsenic level in groundwater. [ABSTRACT FROM AUTHOR]

Abstract: Patterns that maintain and generate biodiversity of macro‐organisms in the Neotropics are widely discussed in the scientific literature, yet the spatial ecology of micro‐organisms is largely unknown. The unique character of the tropical Andes and adjacent Amazon lowlands generates a wide gradient of environmental conditions to advance our understanding of what drives community assembly and diversity processes. We analysed the distribution patterns of benthic diatoms (unicellular siliceous algae) as a model group of microbial passive dispersers, including predictors that describe limnological and geo‐climatic gradients for a total of 113 waterbodies (0–28°S and 58–80°W), including lakes and streams. Complementary multivariate statistical analyses were performed to correlate (1) community composition and (2) diatom species richness with environmental and spatial factors to infer niche‐based and dispersal‐based assembly processes, respectively. Results showed that two gradients structured both diatom assemblages and waterbodies, namely climate and landscape configuration. Variance partitioning revealed that broadscale spatial variables (distance‐based Moran's Eigenvectors) outperformed the two environmental components (limnological and geo‐climatic), suggesting dispersal‐assembled communities. However, diatom assemblages were structured by geo‐climatic (regional) factors in certain lakes in the northern and central Andes, although their effects were partially manifested via local variables after the geographical distances were factored out. In a similar way, climatic and topographic structuring homogenized lake and stream communities within ecoregions, as indicated by the strong overlap between the two community types and the weak correlation between biota and limnological variables. Notably, a significant increase in diatom species richness was related to increased water connectivity, interpreted to indicate that a decrease in the remoteness of the system increase species number. Synthesis. We emphasize the strength of macroecological gradients (landscape configuration and climatic factors) in affecting both diatom diversity and community composition in the South American tropics. In this context, our results and the commonalities of ecoregion patterning with groups of macro‐organisms (vegetation) suggest the need to integrate microbial ecology into a macroecology framework to unravel mechanisms behind diversity gradients. [ABSTRACT FROM AUTHOR]

Purpose: Few studies have been done to investigate the impact of mowing on N2O emissions and the abundance of functional microbial genes, especially in sloping landscapes. This study aims to explore the impact of mowing on key N2O-producing processes under different topographical conditions in a semi-arid grassland.Materials and methods: Soil samples were collected from a semiarid grassland ecosystem in Xilingol region, Inner Mongolia, where long-term management practices including non-mowing and mowing in flat and sloping blocks were conducted. We then determined (1) soil moisture, total carbon (TC) and nitrogen (TN), and mineral N (NH4+-N and NO3−-N) content; (2) the potential N2O emission from nitrification (NN2O) and from denitrification (DN2O) and potential N2 emission (DN2); and (3) the gene abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), the narG (nitrate reductase) gene, and nosZ (nitrous oxide reductase) gene.Results and discussion: Soil moisture and potential N2O emission from nitrification and denitrification were significantly lower in sloping than in flat conditions, whereas the TC, TN, NH4+-N, NO3−-N content, gene abundance of AOA, AOB, narG, and nosZ showed no difference between flat and sloping conditions. Mowing significantly decreased the gene abundance of AOA, AOB, narG in both flat and sloping areas, and significantly decreased potential N2O emissions, especially in sloping areas.Conclusions: The potential N2O emission was significantly lower on sloping than flat grassland. Mowing significantly decreased the potential N2O emissions, especially on sloping grassland. Our results suggest that topographical conditions should be incorporated into methods for estimating N2O emission and land management practices in semiarid grassland. [ABSTRACT FROM AUTHOR]

During the 2012 summer swim season, aquatic venue data and filter backwash samples were collected from 127 metro-Atlanta pools. Last-recorded water chemistry measures indicated 98% (157/161) of samples were from pools with ⩾1 mg/L residual chlorine without stabilized chlorine or ⩾2 mg/L with stabilized chlorine and 89% (144/161) had pH readings 7.2-7.8. These water quality parameters are consistent with the 2016 Model Aquatic Health Code (2nd edition) recommendations. We used previously validated real-time polymerase chain reaction assays for detection of seven enteric microbes, including Escherichia coli, and Pseudomonas aeruginosa. E. coli was detected in 58% (93/161) of samples, signifying that swimmers likely introduced fecal material into pool water. P. aeruginosa was detected in 59% (95/161) of samples, indicating contamination from swimmers or biofilm growth on surfaces. Cryptosporidium spp. and Giardia duodenalis were each detected in approximately 1% of samples. These findings indicate the need for aquatics staff, state and local environmental health practitioners, and swimmers to each take steps to minimize the risk of transmission of infectious pathogens. [ABSTRACT FROM AUTHOR]

Medical researchers are increasingly interested in knowing how the complex community of micro-organisms living on human body impacts human health. Key to this is to understand how the microbes interact with each other. Time-course studies on human microbiome indicate that the composition of microbiome changes over short time periods, primarily as a consequence of synergistic and antagonistic interactions of the members of the microbiome with each other and with the environment. Knowledge of the abundance of bacteria—which are the predominant members of the human microbiome—in such time-course studies along with appropriate mathematical models will allow us to identify key dynamic interaction networks within the microbiome. However, the high-dimensional nature of these data poses significant challenges to the development of such mathematical models. We propose a high-dimensional linear State Space Model (SSM) with a new Expectation-Regularization-Maximization (ERM) algorithm to construct a dynamic icrobial nteraction etwork (MIN). System noise and measurement noise can be separately specified through SSMs. In order to deal with the problem of high-dimensional parameter space in the SSMs, the proposed new ERM algorithm employs the idea of the adaptive LASSO-based variable selection method so that the sparsity property of MINs can be preserved. We performed simulation studies to evaluate the proposed ERM algorithm for variable selection. The proposed method is applied to identify the dynamic MIN from a time-course vaginal microbiome study of women. This method is amenable to future developments, which may include interactions between microbes and the environment. [ABSTRACT FROM AUTHOR]

The degree of polycyclic aromatic hydrocarbon contamination of environmental matrices has increased over the last several years due to increase in industrial activities. Interest has surrounded the occurrence and distribution of polycyclic aromatic hydrocarbons for many decades because they pose a serious threat to the health of humans and ecosystems. The importance of the need for sustainable abatement strategies to alleviate contamination therefore cannot be overemphasised, as daily human activities continue to create pollution from polycyclic aromatic hydrocarbons and impact the natural environment. Globally, attempts have been made to design treatment schemes for the remediation and restoration of contaminated sites. Several techniques and technologies have been proposed and tested over time, the majority of which have significant limitations. This has necessitated research into environmentally friendly and cost-effective clean-up techniques. Bioremediation is an appealing option that has been extensively researched and adopted as it has been proven to be relatively cost-effective, environmentally friendly and is publicly accepted. In this review, the physicochemical properties of some priority polycyclic aromatic hydrocarbons, as well as the pathways and mechanisms through which they enter the soil, river systems, drinking water, groundwater and food are succinctly examined. Their effects on human health, other living organisms, the aquatic ecosystem, as well as soil microbiota are also elucidated. The persistence and bioavailability of polycyclic aromatic hydrocarbons are discussed as well, as they are important factors that influence the rate, efficiency and overall success of remediation. Bioremediation (aerobic and anaerobic), use of biosurfactants and bioreactors, as well as the roles of biofilms in the biological treatment of polycyclic aromatic hydrocarbons are also explored. [ABSTRACT FROM AUTHOR]

Growing evidence points out that the capacity of organisms to acclimate or adapt to new habitat conditions basically depends on their phenomic plasticity attributes, of which their gut commensal microbiota might be an essential impact factor. Especially in aquatic organisms, which are in direct and continual contact with the aquatic environment, the complex and dynamic microbiota have significant effects on health and development. However, an understanding of the relative contribution of internal sorting (host genetic) and colonization (environmental) processes is still unclear. To understand how microbial communities differ in response to rapid environmental change, we surveyed and studied the environmental and gut microbiota of native and habitat-exchanged shrimp (Macrobrachium nipponense) using 16S rRNA amplicon sequencing on the Illumina MiSeq platform. Corresponding with microbial diversity of their living water areas, the divergence in gut microbes of lake-to-river shrimp (CK) increased, while that of river-to-lake shrimp (KC) decreased. Importantly, among the candidate environment specific gut microbes in habitat-exchanged shrimp, over half of reads were associated with the indigenous bacteria in native shrimp gut, yet more candidates presented in CK may reflect the complexity of new environment. Our results suggest that shrimp gut microbiota has high plasticity when its host faces environmental changes, even over short timescales. Further, the changes in external environment might influence the gut microbiome not just by providing environment-associated microbes directly, but also by interfering with the composition of indigenous gut bacteria indirectly. [ABSTRACT FROM AUTHOR]

The mass-ratio and niche complementarity mechanisms drive the influence of litter trait diversity on decomposition. However, the implications of these mechanisms remain poorly understood, as few studies have evaluated their importance relative to environmental conditions and soil decomposers when assessing different processes during decomposition (e.g. C dynamics and N transformations)., We measured litter C and N losses during decomposition in 10 litter mixtures and calculated community-weighted means ( CWM) and dissimilarity (Rao's Q) of 13 litter traits as metrics of the mass-ratio and niche complementarity mechanisms respectively. The 10 litter mixtures were incubated along a regional gradient (10 sites) in southern France over a year, where local environmental conditions (climate and soil parameters), and soil decomposers (microbes, nematodes, and macrofauna) were considered as drivers of decomposition., Sites and litter mixtures represented a wide range of environmental conditions, decomposers, and litter diversity. Litter mixture was the major factor affecting litter C and N loss. N was immobilized during the early decomposition stages (up to c. 40% mass loss), especially in mixtures of low N concentrations. Litter CWM traits were the key drivers of litter C and N loss, but litter trait dissimilarity emerged as a major driver of litter N loss. Macrofauna played a significant role on C and N loss, but environmental conditions exerted a minor influence., Our results highlight that distinct aspects of trait diversity in mixed species litter can play a more important role than environmental conditions and decomposers, which can affect the cycling of litter C and N at regional scales. Rather than opposing mass-ratio and niche complementarity mechanisms, our study shows that both can play a critical role simultaneously in litter decomposition., Synthesis. Our study emphasizes that, in the current context of global biodiversity decline, the mass-ratio and niche complementarity mechanisms should be considered to assess litter decomposition dynamics under global change. As litter diversity mechanisms distinctly affected the cycling of C and N, we recommend taking into account such element-specific effects to improve the prediction of the impacts of biodiversity change on biogeochemical cycles. [ABSTRACT FROM AUTHOR]

Almost one-third of crop yields are lost every year due to microbial alterations and diseases. The main control strategy to limit these losses is the use of an array of chemicals active against spoilage and unwanted pathogenic microorganisms. Their massive use has led to extensive environmental pollution, human poisoning and a variety of diseases. An emerging alternative to this chemical approach is the use of microbial biocontrol agents. Biopesticides have been used with success in several fields, but a better understanding of their mode of action is necessary to better control their activity and increase their use. Very few studies have considered that biofilms are the preferred mode of life of microorganisms in the target agricultural biotopes. Increasing evidence shows that the spatial organization of microbial communities on crop surfaces may drive important bioprotection mechanisms. The aim of this review is to summarize the evidence of biofilm formation by biocontrol agents on crops and discuss how this surface-associated mode of life may influence their biology and interactions with other microorganisms and the host and, finally, their overall beneficial activity. [ABSTRACT FROM AUTHOR]

Background: Despite the important role that microorganisms play in environmental processes, the low percentage of cultured microbes (5%) has limited, until now, our knowledge of their ecological strategies. However, the development of high-throughput sequencing has generated a huge amount of genomic and metagenomic data without the need of culturing that can be used to study ecological questions. This study aims to estimate the functional capabilities, genomic sizes and 16S copy number of different taxa in relation to their ubiquity and their environmental preferences. Results: To achieve this goal, we compiled data regarding the presence of each prokaryotic genera in diverse environments. Then, genomic characteristics such as genome size, 16S rRNA gene copy number, and functional content of the genomes were related to their ubiquity and different environmental preferences of the corresponding taxa. The results showed clear correlations between genomic characteristics and environmental conditions. Conclusions: Ubiquity and adaptation were linked to genome size, while 16S copy number was not directly related to ubiquity. We observed that different combinations of these two characteristics delineate the different environments. Besides, the analysis of functional classes showed some clear signatures linked to particular environments. [ABSTRACT FROM AUTHOR]

Microorganisms are constantly challenged by stressful conditions, such as sugar-rich environments. Such environments can cause an imbalance of biochemical activities and compromise cell multiplication. Gluconacetobacter diazotrophicus PAl 5 is among the most sugar-tolerant bacteria, capable of growing in the presence of up to 876 mM sucrose. However, the molecular mechanisms involved in its response to high sucrose remain unknown. The present work aimed to identify sucrose-induced stress resistance genes in G. diazotrophicus PAl 5. Screening of a Tn5 transposon insertion library identified a mutant that was severely compromised in its resistance to high sucrose concentrations. Molecular characterization revealed that the mutation affected the kupA gene, which encodes a K+ uptake transporter (KupA). Functional complementation of the mutant with the wild type kupA gene recovered the sucrose-induced stress resistance phenotype. High sucrose resistance assay, under different potassium concentrations, revealed that KupA acts as a high-affinity K+ transporter, which is essential for resistance to sucrose-induced stress, when extracellular potassium levels are low. This study is the first to show the essential role of the KupA protein for resistance to sucrose-induced stress in bacteria by acting as a high-affinity potassium transporter in G. diazotrophicus PAl 5. [ABSTRACT FROM AUTHOR]

We present a study on a microbial electrolysis cell with methanogenic microorganisms adapted to reduce CO2 to CH4 with the direct injection of electrons and without the artificial addition of H2 or an additional carbon source except gaseous CO2. This is a new approach in comparison to previous work in which both bicarbonate and gaseous CO2 served as the carbon source. The methanogens used are known to perform well in anaerobic reactors and metabolize H2 and CO2 to CH4 and water. This study shows the biofilm formation of those microorganisms on a carbon felt electrode and the long-term performance for CO2 reduction to CH4 using direct electrochemical reduction. CO2 reduction is performed simply by electron uptake with gaseous CO2 as the sole carbon source in a defined medium. This 'electrometabolism' in such microbial electrolysis cells depends strongly on the potential applied as well as on the environmental conditions. We investigated the performance using different adaption mechanisms and a constant potential of −700 mV vs. Ag/AgCl for CH4 generation at 30-35 °C. The experiments were performed by using two-compartment electrochemical cells. Production rates with Faradaic efficiencies of around 22 % were observed. [ABSTRACT FROM AUTHOR]