Total bacterial diversity in soil and sediment communities—A review

Production, purification, properties and current perspectives for modification and application of microbial lipases

With the industrialization and development of modern science, the application of enzymes as green and environmentally friendly biocatalysts in industry has been increased widely. Among them, lipase (EC. 3.1.1.3) is a very prominent biocatalyst, which has the ability to catalyze the hydrolysis and synthesis of ester compounds. Many lipases have been isolated from various sources, such as animals, plants and microorganisms, among which microbial lipase is the enzyme with the most diverse enzymatic properties and great industrial application potential. It therefore has promising applications in many industries, such as food and beverages, waste treatment, biofuels, leather, textiles, detergent formulations, ester synthesis, pharmaceuticals and medicine. Although many microbial lipases have been isolated and characterized, only some of them have been commercially exploited. In order to cope with the growing industrial demands and overcome these shortcomings to replace traditional chemical catalysts, the preparation of new lipases with thermal/acid-base stability, regioselectivity, organic solvent tolerance, high activity and yield, and reusability through excavation and modification has become a hot research topic.

The origin of suspended particulate matter in the Great Barrier Reef

River run-off has long been regarded as the largest source of organic-rich suspended particulate matter (SPM) in the Great Barrier Reef (GBR), contributing to high turbidity, pollutant exposure and increasing vulnerability of coral reef to climate change. However, the terrestrial versus marine origin of the SPM in the GBR is uncertain. Here we provide multiple lines of evidence (13C NMR, isotopic and genetic fingerprints) to unravel that a considerable proportion of the terrestrially-derived SPM is degraded in the riverine and estuarine mixing zones before it is transported further offshore. The fingerprints of SPM in the marine environment were completely different from those of terrestrial origin but more consistent with that formed by marine phytoplankton. This result indicates that the SPM in the GBR may not have terrestrial origin but produced locally in the marine environment, which has significant implications on developing better-targeted management practices for improving water quality in the GBR.

First Study Case of Microbial Biocontrol Agents Isolated from Aquaponics Through the Mining of High-Throughput Sequencing Data to Control Pythium aphanidermatum on Lettuce

Aquaponics is defined as a sustainable and integrated system that combines fish aquaculture and hydroponic plant production in the same recirculated water loop. A recent study using high-throughput sequencing (HTS) technologies highlighted that microbial communities from an aquaponic system could control one of the most problematic pathogens in soilless lettuce culture, namely, Pythium aphanidermatum. Therefore, this study aims at isolating the microorganisms responsible for this biocontrol action. Based on the most promising genera identified by HTS, an innovative strategy for isolating and testing original biocontrol agents from aquaponic water was designed to control P. aphanidermatum. Eighty-two bacterial strains and 18 fungal strains were isolated, identified by Sanger sequencing, and screened in vivo to control damping-off of lettuce seeds caused by P. aphanidermatum. Out of these 100 isolates, the eight most efficacious ones were selected and further tested individually to control root rot disease caused by the same pathogen at a later stage of lettuce growth. Strains SHb30 (Sphingobium xenophagum), G2 (Aspergillus flavus), and Chito13 (Mycolicibacterium fortuitum) decreased seed damping-off at a better rate than a propamocarb fungicide and a Pseudomonas chlororaphis registered biocontrol agent did. In root rot bioassays, lettuce mortality was prevented by applying strains G2 and Chito13, which were at least as efficacious as the fungicide or biopesticide controls. Lettuce disease symptoms and mortality were eradicated by strain SHb30 in the first bioassay, but not in the second one. These results show that aquaponic systems are promising sources of original biocontrol agents, and that HTS-guided strategies could represent interesting approaches to identify new biocontrol agents.

Distribution and biodegradation potential of polycyclic aromatic hydrocarbons (PAHs) accumulated in media of a stormwater bioretention

Polycyclic aromatic hydrocarbons (PAHs) are a group of organic compounds that can be captured and accumulate in the bioretention cell media, which may lead to secondary pollution and ecological risks. This research aimed to understand the spatial distribution of 16 priority PAHs in bioretention media, identify their sources, evaluate their ecological impact, and assess the potential for their aerobic biodegradation. The highest total PAH concentration (25.5 ± 1.7 μg/g) was observed 1.83 m from the inlet and 10-15 cm deep. The individual PAHs with the highest concentrations were benzo [g,h,i]perylene in February (1.8 ± 0.8 μg/g) and pyrene in June (1.8 ± 0.8 μg/g). Data indicated that primary sources of PAHs were fossil fuel combustion and petroleum. The ecological impact and toxicity of the media were assessed by probable effect concentrations (PECs) and benzo [a]pyrene total toxicity equivalent (BaP-TEQ). The results showed that the concentrations of pyrene and chrysene exceeded the PECs, and the average BaP-TEQ was 1.64 μg/g, primarily caused by benzo [a]pyrene. The functional gene (C12O) of PAH-ring cleaving dioxygenases (PAH-RCD) was present in the surface media, which indicated that aerobic biodegradation of PAHs was possible. Overall, this study revealed the PAHs accumulated most at medium distance and depth, where biodegradation may be limited. Thus, the accumulation of PAHs below the surface of the bioretention cell may need to be considered during long-term operation and maintenance.

Digging and identification of novel microorganisms from the soil environments with high methanol-tolerant lipase production for biodiesel preparation

Converting renewable biomass into carbon-neutral biofuels is one of the most effective strategies to achieve zero carbon emissions and contribute to environmental protection. Microorganisms from the soil were primarily screened on the rhodamine B-plate for highly-active lipase producing strains and re-screened on a tributyrin-methanol plate using crude lipases produced from the initially screened-out strains. The lipase-producing strains with higher methanol-tolerant lipase were identified based on morphological characteristics and 16S rDNA sequencing. The crude lipases with much higher methanol-tolerance from screened top-4 strains, Stenotrophomonas maltophilia D18, Lysinibacillus fusiformis B23, Acinetobacter junii C69, and A. pittii C95 showed temperature optima of 25 °C, 35 °C, 30 °C, and 30 °C at pH 7.0, respectively, while their pH optima were 8.0, 7.0, 7.5, and 7.5 at each optimum temperature, respectively. After 24-h incubation, they retained more than 85% of their original activities in 25%, 15%, 20%, and 20% of methanol, respectively. They catalyzed the conversion of soybean oil into biodiesel by yields of 63.1%, 35.4%, 74.6%, and 78.5% after 24-h reactions, respectively. In conclusion, the as-isolated microorganisms producing high methanol-tolerant lipase are considered promising to provide robust biocatalyst for efficient biodiesel preparation and other industrial applications.

Modeling Root-Knot Nematode Regulation by the Biocontrol Fungus Pochonia chlamydosporia

Two models of increasing complexity were constructed to simulate the interactions between the root-knot nematode (RKN) Meloidogyne incognita and the biocontrol fungus Pochonia chlamydosporia var. catenulata in a rhizosphere microcosm. The models described discrete population dynamics at hourly rates over a 6-month period and were validated using real parasitism and nematode or fungus data. A first, general Pochonia-nematode-root model (GPNR) used five functions and 16 biological constants. The variables and constants describing the RKN life cycle included the rates of egg production, hatching, juvenile (J2), and mature female development, including root or nematode self-density-dependent factors. Other constants accounted for egg parasitism, nematode-induced root losses, growth, and mortalities. The relationship between nematodes and fungal propagules showed density dependence and cyclic variations in time, including an attractor on the propagules and J2 phases space. The simulations confirmed a P. chlamydosporia optimal initial density of 5 · 103 propagules · cc soil-1, as usually applied in assays. The constants used in GPNR showed adherence to the nematode biology, with 103 eggs per egg mass, a 10-day average lifespan of J2, with 2 days required to enter roots, and adult lifespan lasting 24 days. The fungus propagule lifespan was 25 days, with an average feeder root lifespan lasting around 52 days. A second, more complex Pochonia-nematode-root detailed model (GPNRd) was then constructed using eight functions and 23 constants. It was built as GPNR did not allow the evaluation of host prevalence. GPNRd allowed simulations of all RKN life stages and included non-parasitic and parasitic fungus population fractions. Both GPNR and GPNRd matched real J2 and fungus density data observed in a RKN biocontrol assay. Depending on the starting conditions, simulations showed stability in time, interpreted as effective host regulation. GPNRd showed a fungus cyclic relationship with the J2 numbers, with prevalence data close to those observed (38.3 vs. 39.4%, respectively). This model also showed a further density-independent nematode regulation mechanism based on the P. chlamydosporia switch from a non-parasitic to a parasitic trophic behavior. This mechanism supported the biocontrol of M. incognita, also sustained by a concomitant increase of the root density.

Variations in Soil Nutrient Dynamics and Bacterial Communities After the Conversion of Forests to Long-Term Tea Monoculture Systems

The soil microbial community is a key indicator to evaluate the soil health and productivities in agricultural ecosystems. Monoculture and conversions of forests to tea plantations have been widely applied in tea plantation globally, but long-term monoculture of tea plantation could lead to soil degradation and yield decline. Understanding how long-term monoculture systems influence the soil health and ecosystem functions in tea plantation is of great importance for soil environment management. In this study, through the comparison of three independent tea plantations across eastern China composed of varying stand ages (from 3 to 90 years after conversion from forest), we found that long-term tea monoculture led to significant increases in soil total organic carbon (TOC) and microbial nitrogen (MBN). Additionally, the structure, function, and co-occurrence network of soil bacterial communities were investigated by pyrosequencing 16S rRNA genes. The pyrosequencing analysis revealed that the structures and functions of soil bacterial communities were significantly affected by different stand ages, but sampling sites and land-use conversion (from forest to tea plantation) had stronger effects than stand age on the diversity and structure of soil bacterial communities. Soil bacterial diversity can be improved with increasing stand ages in tea plantation. Further RDA analysis revealed that the C and N availability improvement in tea plantation soils led to the variation of structure and function in soil bacterial communities. Moreover, co-occurrence network analysis of soil bacterial communities also demonstrated that interactions among soil bacteria taxa were strengthened with increasing stand age. Our findings suggest that long-term monoculture with proper managements could be beneficial to soil ecosystems by increasing the C and N content and strengthening bacterial associations in tea plantations. Overall, this study provides a comprehensive understanding of the impact of land-use change and long-term monoculture stand age on soil environments in tea plantation.

Spatial Variation and Environmental Parameters Affecting the Abundant and Rare Communities of Bacteria and Archaea in the Sediments of Tropical Urban Reservoirs

Microbial communities in freshwater sediments play an important role in organic matter remineralization, contributing to biogeochemical cycles, nutrient release, and greenhouse gases emissions. Bacterial and archaeal communities might show spatial or seasonal patterns and were shown to be influenced by distinct environmental parameters and anthropogenic activities, including pollution and damming. Here, we determined the spatial variation and the environmental variables influencing the abundant and rare bacterial and archaeal communities in the sediments of eutrophic-hypereutrophic reservoirs from a tropical urban area in Brazil. The most abundant microbes included mainly Anaerolineae and Deltaproteobacteria genera from the Bacteria domain, and Methanomicrobia genera from the Archaea domain. Microbial communities differed spatially in each reservoir, reflecting the establishment of specific environmental conditions. Locations with better or worst water quality, or close to a dam, showed more distinct microbial communities. Besides the water column depth, microbial communities were affected by some pollution indicators, including total phosphorus, orthophosphate, electrical conductivity, and biochemical oxygen demand. Distinct proportions of variation were explained by spatial and environmental parameters for each microbial community. Furthermore, spatial variations in environmental parameters affecting these communities, especially the most distinct ones, contributed to microbial variations mediated by spatial and environmental properties together. Finally, our study showed that different pressures in each reservoir affected the sediment microbiota, promoting different responses and possible adaptations of abundant and rare bacterial and archaeal communities.

Environmental and Human Microbiome for Health

Microorganisms are an essential part of life on the earth and can exist in association with virtually any living thing. The environmental microbiome is much more diverse than the human microbiome. It is reported that most microbes existing in the environment are difficult to culture in the laboratory. Whereas both pathogenic and beneficial microbes may be prevailing in the environment, the human body can have three categories of microbes- beneficial, pathogenic, and opportunistic pathogenic. With at least 10-fold more cells than human cells, microbes as normal flora are critical for human survival. The microbes present in the human body play a crucial role in maintaining human health, and the environmental microbiome influences the human microbiome makeup. The interaction between the environmental and human microbiome highly influences human health, however it is poorly understood. In addition, as an established infection is associated with health-seeking behavior, a large number of studies have focused on the transmission and dynamics of infectious microorganisms than the noninfectious or beneficial ones. This review will summarize how the interaction between the environmental and human microbiome affects human health and identify approaches that might be beneficial for humans to improve health by being exposed to the natural environment.

Needles in haystacks: reevaluating old paradigms for the discovery of bacterial secondary metabolites

Covering: up to 2021Natural products research is in the midst of a renaissance ushered in by a modern understanding of microbiology and the technological explosions of genomics and metabolomics. As the exploration of uncharted chemical space expands into high-throughput discovery campaigns, it has become increasingly clear how design elements influence success: (bio)geography, habitat, community dynamics, culturing/induction methods, screening methods, dereplication, and more. We explore critical considerations and assumptions in natural products discovery. We revisit previous estimates of chemical rediscovery and discuss their relatedness to study design and producer taxonomy. Through frequency analyses of biosynthetic gene clusters in publicly available genomic data, we highlight phylogenetic biases that influence rediscovery rates. Through selected examples of how study design at each level determines discovery outcomes, we discuss the challenges and opportunities for the future of high-throughput natural product discovery.

An uncharacterized protein from the metagenome with no obvious homology to known lipases shows excellent alkaline lipase properties and potential applications in the detergent industry

A novel lipase, Lip486, which has no obvious homology with known lipases, was discovered using functional metagenomics technology. Phylogenetic tree analysis suggested that the enzyme belongs to a new subfamily called lipolytic enzyme family II. To explore the enzymatic properties, lip486 was expressed heterologously and efficiently in Escherichia coli. The recombinant enzyme displayed the highest activity on the substrate p-nitrophenyl caprate with a carbon chain length of 10, and its optimum temperature and pH were 53 °C and 8.0, respectively. The recombinant Lip486 showed good activity and stability in strong alkaline and medium-low-temperature environments. The results of compatibility and soaking tests showed that the enzyme had good compatibility with 4 kinds of commercial detergents, and an appropriate soaking time could further improve the enzyme activity. Oil stain removal test results for a cotton cloth indicated that the washing performance of commercial laundry detergent supplemented with Lip486 was further improved. In addition, as one of the smallest lipases found to date, Lip486 also has the advantages of high yield, good stability and easy molecular modification. These characteristics reflect the good application prospects for Lip486 in the detergent and other industries in the future.

Extremophiles in Soil Communities of Former Copper Mining Sites of the East Harz Region (Germany) Reflected by Re-Analyzed 16S rRNA Data

The east and southeast rim of Harz mountains (Germany) are marked by a high density of former copper mining places dating back from the late 20th century to the middle age. A set of 18 soil samples from pre- and early industrial mining places and one sample from an industrial mine dump have been selected for investigation by 16S rRNA and compared with six samples from non-mining areas. Although most of the soil samples from the old mines show pH values around 7, RNA profiling reflects many operational taxonomical units (OTUs) belonging to acidophilic genera. For some of these OTUs, similarities were found with their abundances in the comparative samples, while others show significant differences. In addition to pH-dependent bacteria, thermophilic, psychrophilic, and halophilic types were observed. Among these OTUs, several DNA sequences are related to bacteria which are reported to show the ability to metabolize special substrates. Some OTUs absent in comparative samples from limestone substrates, among them Thaumarchaeota were present in the soil group from ancient mines with pH > 7. In contrast, acidophilic types have been found in a sample from a copper slag deposit, e.g., the polymer degrading bacterium Granulicella and Acidicaldus, which is thermophilic, too. Soil samples of the group of pre-industrial mines supplied some less abundant, interesting OTUs as the polymer-degrading Povalibacter and the halophilic Lewinella and Halobacteriovorax. A particularly high number of bacteria (OTUs) which had not been detected in other samples were found at an industrial copper mine dump, among them many halophilic and psychrophilic types. In summary, the results show that soil samples from the ancient copper mining places contain soil bacterial communities that could be a promising source in the search for microorganisms with valuable metabolic capabilities.

Global Trends of Benthic Bacterial Diversity and Community Composition Along Organic Enrichment Gradients of Salmon Farms

The analysis of benthic bacterial community structure has emerged as a powerful alternative to traditional microscopy-based taxonomic approaches to monitor aquaculture disturbance in coastal environments. However, local bacterial diversity and community composition vary with season, biogeographic region, hydrology, sediment texture, and aquafarm-specific parameters. Therefore, without an understanding of the inherent variation contained within community complexes, bacterial diversity surveys conducted at individual farms, countries, or specific seasons may not be able to infer global universal pictures of bacterial community diversity and composition at different degrees of aquaculture disturbance. We have analyzed environmental DNA (eDNA) metabarcodes (V3-V4 region of the hypervariable SSU rRNA gene) of 138 samples of different farms located in different major salmon-producing countries. For these samples, we identified universal bacterial core taxa that indicate high, moderate, and low aquaculture impact, regardless of sampling season, sampled country, seafloor substrate type, or local farming and environmental conditions. We also discuss bacterial taxon groups that are specific for individual local conditions. We then link the metabolic properties of the identified bacterial taxon groups to benthic processes, which provides a better understanding of universal benthic ecosystem function(ing) of coastal aquaculture sites. Our results may further guide the continuing development of a practical and generic bacterial eDNA-based environmental monitoring approach.

Biological nitrification inhibition in the rhizosphere: determining interactions and impact on microbially mediated processes and potential applications

Nitrification is the microbial conversion of reduced forms of nitrogen (N) to nitrate (NO3-), and in fertilized soils it can lead to substantial N losses via NO3- leaching or nitrous oxide (N2O) production. To limit such problems, synthetic nitrification inhibitors have been applied but their performance differs between soils. In recent years, there has been an increasing interest in the occurrence of biological nitrification inhibition (BNI), a natural phenomenon according to which certain plants can inhibit nitrification through the release of active compounds in root exudates. Here, we synthesize the current state of research but also unravel knowledge gaps in the field. The nitrification process is discussed considering recent discoveries in genomics, biochemistry and ecology of nitrifiers. Secondly, we focus on the 'where' and 'how' of BNI. The N transformations and their interconnections as they occur in, and are affected by, the rhizosphere, are also discussed. The NH4+ and NO3- retention pathways alternative to BNI are reviewed as well. We also provide hypotheses on how plant compounds with putative BNI ability can reach their targets inside the cell and inhibit ammonia oxidation. Finally, we discuss a set of techniques that can be successfully applied to solve unresearched questions in BNI studies.

Soil microbial community structure and functionality changes in response to long-term metal and radionuclide pollution

Microbial communities are essential for a healthy soil ecosystem. Metals and radionuclides can exert a persistent pressure on the soil microbial community. However, little is known on the effect of long‐term co‐contamination of metals and radionuclides on the microbial community structure and functionality. We investigated the impact of historical discharges of the phosphate and nuclear industry on the microbial community in the Grote Nete river basin in Belgium. Eight locations were sampled along a transect to the river edge and one location further in the field. Chemical analysis demonstrated a metal and radionuclide contamination gradient and revealed a distinct clustering of the locations based on all metadata. Moreover, a relation between the chemical parameters and the bacterial community structure was demonstrated. Although no difference in biomass was observed between locations, cultivation‐dependent experiments showed that communities from contaminated locations survived better on singular metals than communities from control locations. Furthermore, nitrification, a key soil ecosystem process seemed affected in contaminated locations when combining metadata with microbial profiling. These results indicate that long‐term metal and radionuclide pollution impacts the microbial community structure and functionality and provides important fundamental insights into microbial community dynamics in co‐metal‐radionuclide contaminated sites.

La milpa como modelo para el estudio de la microbiodiversidad e interacciones planta-bacteria

La microbiología agrícola busca reemplazar a los agroquímicos por microorganismos o sus productos como agentes de control biológico, debido a que el uso de tecnologías de la revolución verde tiene efectos negativos sobre el ambiente, los productores y sus familias, los consumidores y la salud de los cultivos. Sin embargo, el conocimiento actual acerca de las interacciones benéficas planta-bacteria en ambientes complejos es limitado e insuficiente, para lograr el éxito esperado de los productos biológicos. Las milpas son agroecosistemas tradicionales donde se cultivan diversas variedades de maíz nativo con otras especies asociadas; no se utiliza riego, ni labranza y aunque su aplicación va en aumento, comúnmente no se utilizan agroquímicos; por esto, la milpa representa una fuente de conocimiento sobre prácticas sustentables. Recientemente, se han descrito cambios en las comunidades microbianas de los sistemas agrícolas a causa de la modernización y a la domesticación de las plantas. En la milpa, también se han identificado interacciones benéficas planta-bacteria que parecen haberse perdido en los cultivos modernos. En esta revisión, discutimos las estrategias clásicas y modernas de la microbiología agrícola que pueden ser aplicadas en el estudio de la milpa. El establecimiento de la milpa como modelo de estudio de las interacciones planta-bacteria puede resultar en la generación del conocimiento necesario para disminuir el uso de agroquímicos en los sistemas agrícolas modernos, así como evitar su creciente uso en las milpas.

Development and Analysis of a Stable, Reduced Complexity Model Soil Microbiome

The soil microbiome is central to the cycling of carbon and other nutrients and to the promotion of plant growth. Despite its importance, analysis of the soil microbiome is difficult due to its sheer complexity, with thousands of interacting species. Here, we reduced this complexity by developing model soil microbial consortia that are simpler and more amenable to experimental analysis but still represent important microbial functions of the native soil ecosystem. Samples were collected from an arid grassland soil and microbial communities (consisting mainly of bacterial species) were enriched on agar plates containing chitin as the main carbon source. Chitin was chosen because it is an abundant carbon and nitrogen polymer in soil that often requires the coordinated action of several microorganisms for complete metabolic degradation. Several soil consortia were derived that had tractable richness (30–50 OTUs) with diverse phyla representative of the native soil, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia. The resulting consortia could be stored as glycerol or lyophilized stocks at −80°C and revived while retaining community composition, greatly increasing their use as tools for the research community at large. One of the consortia that was particularly stable was chosen as a model soil consortium (MSC-1) for further analysis. MSC-1 species interactions were studied using both pairwise co-cultivation in liquid media and during growth in soil under several perturbations. Co-abundance analyses highlighted interspecies interactions and helped to define keystone species, including Mycobacterium, Rhodococcus, and Rhizobiales taxa. These experiments demonstrate the success of an approach based on naturally enriching a community of interacting species that can be stored, revived, and shared. The knowledge gained from querying these communities and their interactions will enable better understanding of the soil microbiome and the roles these interactions play in this environment.

Organic Amendments for Pathogen and Nematode Control

The loss of methyl bromide as a soil fumigant and minimal advances in the development and registration of new chemical fumigants has resulted in a resurgence of interest in the application of organic amendments (OAs) for soilborne plant pathogen and plant-parasitic nematode management. Significant progress has been made in the characterization of OAs, application of strategies for their use, and elucidation of mechanisms by which they suppress soilborne pests. Nonetheless, their utility is limited by the variability of disease control, expense, and the logistics of introducing them into crop production systems. Recent advances in molecular techniques have led to significant progress in the elucidation of the role of bacteria and fungi and their metabolic products on disease suppression with the addition of OAs. Biosolarization and anaerobic soil disinfestation, developed to manipulate systems and favor beneficial microorganisms to maximize their impact on plant pathogens, are built on a strong historical research foundation in OAs and the physical, chemical, and biological characteristics of disease-suppressive soils. This review focuses on recent applications of OAs and their potential for the management of soilborne plant pathogens and plant-parasitic nematodes, with emphasis primarily on annual fruit and vegetable production systems.

Targeted Cell Sorting Combined With Single Cell Genomics Captures Low Abundant Microbial Dark Matter With Higher Sensitivity Than Metagenomics

Rare members of environmental microbial communities are often overlooked and unexplored, primarily due to the lack of techniques capable of acquiring their genomes. Chloroflexi belong to one of the most understudied phyla, even though many of its members are ubiquitous in the environment and some play important roles in biochemical cycles or biotechnological applications. We here used a targeted cell-sorting approach, which enables the selection of specific taxa by fluorescent labeling and is compatible with subsequent single-cell genomics, to enrich for rare Chloroflexi species from a wastewater-treatment plant and obtain their genomes. The combined workflow was able to retrieve a substantially higher number of novel Chloroflexi draft genomes with much greater phylogenetical diversity when compared to a metagenomics approach from the same sample. The method offers an opportunity to access genetic information from rare biosphere members which would have otherwise stayed hidden as microbial dark matter and can therefore serve as an essential complement to cultivation-based, metagenomics, and microbial community-focused research approaches.

Exploitation of Potential Extremophiles for Bioremediation of Xenobiotics Compounds: A Biotechnological Approach

Microorganisms that are capable of live and adapt in hostile habitats of different environmental factors such as extremes temperature, salinity, nutrient availability and pressure are known as extremophiles. Exposure to xenobiotic compounds is global concern influencing the world population as a health hazard. Hence their removal is warranted using biological means that is very sustainable, potentially cost-effective and eco-friendly. Due to adaptation in extreme environments and unique defense mechanisms, they are receiving more attention for the bioremediation of the xenobiotic compounds. They possess robust enzymatic and biocatalytic systems that make them suitable for the effective removal of pollutants from the contaminated environment. Additionally, the extremophiles act as microfactories having specific genetic and biotechnological potential for the production of biomolecules. This mini review will provide an overview of microbial degradation metabolic pathways for bioremediation along with the molecular and physiological properties of diverse extremophiles from variety of habitats. Furthermore, the factors affecting the bioremediation process is also summarized.

Sclerotia of a phytopathogenic fungus restrict microbial diversity and improve soil health by suppressing other pathogens and enriching beneficial microorganisms

Sclerotinia sclerotiorum, a notorious soil-borne pathogen of various important crops, produces numerous sclerotia to oversummer in the soil. Considering that sclerotia may also be attacked by other microbes in the soil, we hypothesized that sclerotia in soil may affect the community of soil microbes directly and/or indirectly. In this study, we inoculated sclerotia of S. sclerotiorum in soil collected from the field to observe changes in microbial diversity over three months using 16S rRNA and ITS2 sequencing techniques. Alpha diversity indices exhibited a decline in the diversity of microbial communities, while permanova results confirmed a significant difference in the microbial communities of sclerotia-amended and non-amended soil samples. In sclerotia-amended soil, fungal diversity showed enrichment of antagonists such as Clonostachys, Trichoderma, and Talaromyces and a drastic reduction in the plant pathogenic microbes compared to the non-amended soil. Sclerotia not only activated the antagonists but also enhanced the abundance of plant growth-promoting bacteria, such as Chitinophaga, Burkholderia, and Dyella. Moreover, the presence of sclerotia curtailed the growth of several notorious plant pathogenic fungi belonging to various genera such as Fusarium, Colletotrichum, Cladosporium, Athelia, Alternaria, and Macrophomina. Thus, we conclude that S. sclerotiorum when dormant in soil can reduce the diversity of soil microbes, including suppressing plant pathogens and enriching beneficial microbes. To the best of our knowledge, this is the first time a plant pathogen has been found in soil that can significantly suppress other pathogens. Our findings may provide novel cues to understand the ecology of crop pathogens in soil and maintaining soil conditions that could be beneficial for constructing a healthy soil microorganism community required for mitigating soil-borne diseases.

Pollution Gradients Altered the Bacterial Community Composition and Stochastic Process of Rural Polluted Ponds

Understanding the effects of pollution on ecological communities and the underlying mechanisms that drive them will helpful for selecting a method to mediate polluted ecosystems. Quantifying the relative importance of deterministic and stochastic processes is a very important issue in ecology. However, little is known about their effects on the succession of microbial communities in different pollution levels rural ponds. Also, the processes that govern bacterial communities in polluted ponds are poorly understood. In this study, the microbial communities in water and sediment from the ponds were investigated by using the 16S rRNA gene high-throughput sequencing technology. Meanwhile, we used null model analyses based on a taxonomic and phylogenetic metrics approach to test the microbial community assembly processes. Pollution levels were found to significantly alter the community composition and diversity of bacteria. In the sediment samples, the bacterial diversity indices decreased with increasing pollutant levels. Between-community analysis revealed that community assembly processes among water and sediment samples stochastic ratio both gradually decreased with the increased pollution levels, indicating a potential deterministic environmental filtering that is elicited by pollution. Our results identified assemblage drivers of bacterial community is important for improving the efficacies of ecological evaluation and remediation for contaminated freshwater systems.

Metatranscriptomics: an approach for retrieving novel eukaryotic genes from polluted and related environments

Metatranscriptomics, a subset of metagenomics, provides valuable information about the whole gene expression profiling of complex microbial communities of an ecosystem. Metagenomic studies mainly focus on the genomic content and identification of microbes present within a community, while metatranscriptomics provides the diversity of the active genes within such community, their expression profile and how these levels change due to change in environmental conditions. Metatranscriptomics has been applied to different types of environments, from the study of human microbiomes, to those found in plants, animals, within soils and in aquatic systems. Metatranscriptomics, based on the utilization of mRNA isolated from environmental samples, is a suitable approach to mine the eukaryotic gene pool for genes of biotechnological relevance. Also, it is imperative to develop different bioinformatic pipelines to analyse the data obtained from metatranscriptomic analysis. In the present review, we summarise the metatranscriptomics applied to soil environments to study the functional diversity, and discuss approaches for isolating the genes involved in organic matter degradation and providing tolerance to toxic metals, role of metatranscriptomics in microbiome research, various bioinformatics pipelines used in data analysis and technical challenges for gaining biologically meaningful insight of this approach.

Metagenomics: Is it a powerful tool to obtain lipases for application in biocatalysis?

In recent years, metagenomic strategies have been widely used to isolate and identify new enzymes from uncultivable components of microbial communities. Among these enzymes, various lipases have been obtained from metagenomic libraries from different environments and characterized. Although many of these lipases have characteristics that could make them interesting for application in biocatalysis, relatively little work has been done to evaluate their potential to catalyze industrially important reactions. In the present article, we highlight the latest research on lipases obtained through metagenomic tools, focusing on studies of activity and stability and investigations of application in biocatalysis. We also discuss the challenges of metagenomic approaches for the bioprospecting of new lipases.

When Is A Lineage A Species? A Case Study In Myxacorys gen. nov. (Synechococcales: Cyanobacteria) With The Description of Two New Species From The Americas

Soil cyanobacteria are crucial components of biological soil crusts and carry out many functions in dryland ecosystems. Despite this importance, their taxonomy and population genetics remain poorly known. We isolated 42 strains of simple filamentous cyanobacteria previously identified as Pseudophormidium hollerbachianum from 26 desert locations in the North and South America and characterized these strains using a total evidence approach, that is, using both morphological and molecular data to arrive at taxonomic decisions. Based on a phylogenetic analysis of 16S rRNA gene sequences, we propose and characterize Myxacorys gen. nov. with two new species Myxacorys chilensis, the generitype, and M. californica. We also found distinct 16S-23S ITS sequence variability within species in our dataset. Especially interesting was the presence of two distinct lineages of M. californica obtained from locations in close spatial proximity (within a few meters to kilometers from each other) suggesting niche differentiation. The detection of such unrecognized lineage-level variability in soil cyanobacteria has important implications for biocrust restoration practices and conservation efforts.

Predicting provenance of forensic soil samples: Linking soil to ecological habitats by metabarcoding and supervised classification

Environmental DNA (eDNA) is increasingly applied in ecological studies, including studies with the primary purpose of criminal investigation, in which eDNA from soil can be used to pair samples or reveal sample provenance. We collected soil eDNA samples as part of a large national biodiversity research project across 130 sites in Denmark. We investigated the potential for soil eDNA metabarcoding in predicting provenance in terms of environmental conditions, habitat type and geographic regions. We used linear regression for predicting environmental gradients of light, soil moisture, pH and nutrient status (represented by Ellenberg Indicator Values, EIVs) and Quadratic Discriminant Analysis (QDA) to predict habitat type and geographic region. eDNA data performed relatively well as a predictor of environmental gradients (R² > 0.81). Its ability to discriminate between habitat types was variable, with high accuracy for certain forest types and low accuracy for heathland, which was poorly predicted. Geographic region was also less accurately predicted by eDNA. We demonstrated the application of provenance prediction in forensic science by evaluating and discussing two mock crime scenes. Here, we listed the plant species from annotated sequences, which can further aid in identifying the likely habitat or, in case of rare species, a geographic region. Predictions of environmental gradients and habitat types together give an overall accurate description of a crime scene, but care should be taken when interpreting annotated sequences, e.g. due to erroneous assignments in GenBank. Our approach demonstrates that important habitat properties can be derived from soil eDNA, and exemplifies a range of potential applications of eDNA in forensic ecology.

Competition and predation as possible causes of bacterial rarity

We assembled communities of bacteria and exposed them to different nutrient concentrations with or without predation by protists. Taxa that were rare in the field were less abundant at low nutrient concentrations than common taxa, independent of predation. However, some taxa that were rare in the field became highly abundant in the assembled communities, especially under ample nutrient availability. This high abundance points at a possible competitive advantage of some rare bacterial taxa under nutrient-rich conditions. In contrast, the abundance of most rare bacterial taxa decreased at low resource availability. Since low resource availability will be the prevailing situation in most soils, our data suggests that under those conditions poor competitiveness for limiting resources may contribute to bacterial rarity. Interestingly, taxa that were rare in the field and most successful under predator-free conditions in the lab also tended to be more reduced by predation than common taxa. This suggests that predation contributes to rarity of bacterial taxa in the field. We further discuss whether there may be a trade-off between competitiveness and predation resistance. The substantial variability among taxa in their responses to competition and predation suggests that other factors, for example abiotic conditions and dispersal ability, also influence the local abundance of soil bacteria.

A soil bacterium alters sex determination and rhizoid development in gametophytes of the fern Ceratopteris richardii

Gametophytes of the fern Ceratopteris richardii develop into either hermaphrodites or males. As hermaphrodites develop, they secrete antheridiogen, or A_CE, into the environment, inducing male development in undifferentiated gametophytes. Hermaphrodites are composed of archegonia, antheridia, rhizoids and a notch meristem, while males consist of antheridia and rhizoids. Much of the research on sexual and morphological development concerns gametophytes grown in sterile environments. Using biochemical and molecular techniques we identify a soil bacterium and explore its effects on sexual and rhizoid development. Hermaphrodite and male gametophytes were exposed to this bacterium and the effects on sexual development, rhizoid length and rhizoid number were explored. The bacterium was identified as a pseudomonad, Pseudomonas nitroreducens. Gametophytes grown in the presence of the pseudomonad were more likely to develop into hermaphrodites across all gametophyte densities. Across all gametophyte sizes, hermaphrodites had rhizoids that were 2.95× longer in the presence of the pseudomonad while males had rhizoids that were 2.72× longer in the presence of the pseudomonad. Both hermaphrodite and male gametophytes developed fewer rhizoids in the presence of the pseudomonad. Control hermaphrodites produced 1.23× more rhizoids across all gametophyte sizes. For male gametophytes grown in the absence of the pseudomonad, the rate of increase in the number of rhizoids was greater with increasing size in the control than the rate of increase in males grown in the presence of the pseudomonad. The pseudomonad may be acting on gametophyte sexual development via several potential mechanisms: degradation of A_CE, changes in nutrient availability or phytohormone production. The pseudomonad may also increase rhizoid number through production of phytohormones or changes in nutrient availability.

Community composition of marine and brackish water ammonia-oxidizing consortia developed for aquaculture application

To mitigate the toxicity of ammonia in aquaculture systems, marine and brackish water ammonia-oxidizing bacterial consortia have been developed and are used for activation of nitrifying bioreactors integrated to recirculating aquaculture systems. To shed more light on to these biological entities, diversity of both the consortia were analyzed based on random cloning of 16S rRNA gene and ammonia-oxidizing bacterial specific amoA gene sequences. The dendrograms of representative clones on the basis of amplified ribosomal DNA restriction analysis generated 22 and 19 clusters for marine and brackish water nitrifying consortia, respectively. Phylogenetic analysis demonstrated the presence of various autotrophic nitrifiers belonging to α-, β- and γ-Proteobacteria, anaerobic ammonia oxidizers, heterotrophic denitrifiers, Bacteroidetes, and Actinobacteria. Distribution patterns of the organisms within the two consortia were determined using the software Geneious and diversity indices were investigated using Mega 5.0, VITCOMIC and Primer 7. The abundance of ammonia oxidizers was found in the order of 2.21 ± 0.25 × 10⁹ copies/g wet weight of marine consortium and 6.20 ± 0.23 × 10⁷ copies/g of brackish water consortium. Besides, marine ammonia-oxidizing consortium exhibited higher mean population diversity and Shannon Wiener diversity than the brackish water counterparts.

Divergence in energy sources for Prochilodus lineatus (Characiformes: Prochilodontidae) in Neotropical floodplains

ABSTRACT The stable carbon isotopic variability and the contributions of autochthonous (sediment microbial biomass, phytoplankton, and periphyton) and allochthonous (soil microbial biomass) sources available to the detritivorous fish Prochilodus lineatus were investigated in three environments of the floodplain of the Upper Paraná River. The isotopic composition of carbon sources and fish varied significantly among the studied environments. The autochthonous resources, represented by the phytoplankton, were the most assimilated by the species, followed by periphyton and sediment microbial biomass. The species used the sources differently in each environment. This study suggests that the inherent characteristics of this area, as well as the size of the watershed, the dry season, anthropogenic actions, and phytoplankton productivity, favor the use of autochthonous resources by the species studied. Therefore, studies in the floodplain should employ an eco-hydrological approach that quantifies the magnitude of energy subsidies, as well as an access route to consumers, knowledge about the selectivity of detritivorous species and the effects of different land uses.

Local and Regional Scale Heterogeneity Drive Bacterial Community Diversity and Composition in a Polar Desert

The distribution of organisms in an environment is neither uniform nor random but is instead spatially patterned. The factors that control this patterning are complex and the underlying mechanisms are poorly understood. Soil microbes are critical to ecosystem function but exhibit highly complex distributions and community dynamics due in large part to the scale-dependent effects of environmental heterogeneity. To better understand the impact of environmental heterogeneity on the distribution of soil microbes, we sequenced the 16S rRNA gene from bacterial communities in the microbe-dominated polar desert ecosystem of the McMurdo Dry Valleys (MDV), Antarctica. Significant differences in key edaphic variables and alpha diversity were observed among the three lake basins of the Taylor Valley (Kruskal-Wallis; pH: χ2 = 68.89, P < 0.001, conductivity: χ2 = 35.03, P < 0.001, observed species: χ2 = 7.98, P = 0.019 and inverse Simpson: χ2 = 18.52, P < 0.001) and each basin supported distinctive microbial communities (ANOSIM R = 0.466, P = 0.001, random forest ratio of 14.1). However, relationships between community structure and edaphic characteristics were highly variable and contextual, ranging in magnitude and direction across regional, basin, and local scales. Correlations among edaphic factors (pH and soil conductivity) and the relative abundance of specific phyla were most pronounced along local environmental gradients in the Lake Fryxell basin where Acidobacteria, Bacteroidetes, and Proteobacteria declined while Deinococcus-Thermus and Gemmatimonadetes increased with soil conductivity (all P < 0.1). Species richness was most strongly related to the soil conductivity gradient present within this study system. We suggest that the relative importance of pH versus soil conductivity in structuring microbial communities is related to the length of edaphic gradients and the spatial scale of sampling. These results highlight the importance of conducting studies over large ranges of key environmental gradients and across multiple spatial scales to assess the influence of environmental heterogeneity on the composition and diversity of microbial communities.

Diversity of Gene Clusters for Polyketide and Nonribosomal Peptide Biosynthesis Revealed by Metagenomic Analysis of the Yellow Sea Sediment

Polyketides (PKs) and nonribosomal peptides (NRPs) are widely applied as drugs in use today, and one potential source for novel PKs and NRPs is the marine sediment microbes. However, the diversities of microbes and their PKs and NRPs biosynthetic genes in the marine sediment are rarely reported. In this study, 16S rRNA gene fragments of the Yellow Sea sediment were analyzed, demonstrating that Proteobacteria and Bacteroidetes accounted for 62% of all the bacterial species and Actinobacteria bacteria which were seen as the typical PKs and NRPs producers only accounted for 0.82% of all the bacterial species. At the same time, PKs and NRPs diversities were evaluated based on the diversity of gene fragments of type I polyketide synthase (PKS) ketosynthase domain (KS), nonribosomal peptide synthetase (NRPS) adenylation domain (AD), and dTDP-glucose-4,6-dehydratase (dTGD). The results showed that AD genes and dTGD genes were abundant and some of them had less than 50% identities with known ones; By contrast, only few KS genes were identified and most of them had more than 60% identities with known KS genes. Moreover, one 70,000-fosmid clone library was further constructed to screen for fosmid clones harboring PKS or NRPS gene clusters of the Yellow Sea sediment. Nine selected fosmid clones harboring KS or AD were sequenced, and three of the clones were assigned to Proteobacteria. Though only few Actinobacteria 16S rRNA gene sequences were detected in the microbial community, five of the screened fosmid clones were assigned to Actinobacteria. Further assembly of the 9 fosmid clones resulted in 11 contigs harboring PKS, NRPS or hybrid NPRS-PKS gene clusters. These gene clusters showed less than 60% identities with the known ones and might synthesize novel natural products. Taken together, we revealed the diversity of microbes in the Yellow Sea sediments and found that most of the microbes were uncultured. Besides, evaluation of PKS and NRPS biosynthetic gene clusters suggested that the marine sediment might have the ability to synthesize novel natural products and more NRPS gene clusters than PKS gene clusters distributed in this environment.

Biophysical processes supporting the diversity of microbial life in soil

Soil, the living terrestrial skin of the Earth, plays a central role in supporting life and is home to an unimaginable diversity of microorganisms. This review explores key drivers for microbial life in soils under different climates and land-use practices at scales ranging from soil pores to landscapes. We delineate special features of soil as a microbial habitat (focusing on bacteria) and the consequences for microbial communities. This review covers recent modeling advances that link soil physical processes with microbial life (termed biophysical processes). Readers are introduced to concepts governing water organization in soil pores and associated transport properties and microbial dispersion ranges often determined by the spatial organization of a highly dynamic soil aqueous phase. The narrow hydrological windows of wetting and aqueous phase connectedness are crucial for resource distribution and longer range transport of microorganisms. Feedbacks between microbial activity and their immediate environment are responsible for emergence and stabilization of soil structure-the scaffolding for soil ecological functioning. We synthesize insights from historical and contemporary studies to provide an outlook for the challenges and opportunities for developing a quantitative ecological framework to delineate and predict the microbial component of soil functioning.

A Cell-Cell Communication-Based Screening System for Novel Microbes with Target Enzyme Activities

The development of synthetic biological devices has increased rapidly in recent years and the practical benefits of such biological devices are becoming increasingly clear. Here, we further improved the design of a previously reported high-throughput genetic enzyme screening system by investigating device-compatible biological components and phenol-mediated cell-cell communication, both of which increased the efficiency and practicality of the screening device without requiring the use of flow cytometry analysis. A sensor cell was designed to detect novel microbes with target enzyme activities on solid media by forming clear, circular colonies with fluorescence around the unknown microbes producing target enzymes. This mechanism of detection was enabled by the combination of pre-effector phenolic substrate treatment in the presence of target enzyme-producing microbes and control of the growth and fluorescence of remote sensor cells via phenol-mediated cell-cell communication. The sensor cells were applied to screen soil bacteria with phosphatase activity using phenyl phosphate as phenolic substrates. The sensor cells facilitated successful visualization of phosphatase activity in unknown microbes, which were identified by 16S rRNA analysis. Enzyme activity assays confirmed that the proposed screening technique was able to find 23 positive clones out of 33 selected colonies. Since many natural enzymatic reactions produce phenolic compounds from phenol-derived substrates, we anticipate that the proposed technique may have broad applications in the assessment and screening of novel microbes with target enzymes of interest. This method also can provide insights into the identification of novel enzymes for which screening assays are not yet available.

Analysis of Plant Growth-Promoting Effects of Fluorescent Pseudomonas Strains Isolated from Mentha piperita Rhizosphere and Effects of Their Volatile Organic Compounds on Essential Oil Composition

Many species or strains of the genus Pseudomonas have been characterized as plant growth promoting rhizobacteria (PGPR). We used a combination of phenotypic and genotypic techniques to analyze the community of fluorescent Pseudomonas strains in the rhizosphere of commercially grown Mentha piperita (peppermint). Biochemical techniques, Amplified rDNA Restriction Analysis (ARDRA), and 16S rRNA gene sequence analysis revealed that the majority of the isolated native fluorescent strains were P. putida. Use of two Repetitive Sequence-based PCR (rep-PCR) techniques, BOX-PCR and ERIC-PCR, allowed us to evaluate diversity among the native strains and to more effectively distinguish among them. PGPR activity was tested for the native strains and reference strain P. fluorescens WCS417r. Micropropagated M. piperita plantlets were exposed to microbial volatile organic compounds (mVOCs) emitted by the bacterial strains, and plant biomass parameters and production of essential oils (EOs) were measured. mVOCs from 11 of the native strains caused an increase in shoot fresh weight. mVOCs from three native strains (SJ04, SJ25, SJ48) induced changes in M. pierita EO composition. The mVOCs caused a reduction of metabolites in the monoterpene pathway, for example menthofuran, and an increase in menthol production. Menthol production is the primary indicator of EO quality. The mVOCs produced by native strains SJ04, SJ25, SJ48, and strain WCS417r were analyzed. The obtained mVOC chromatographic profiles were unique for each of the three native strains analyzed, containing varying hydrocarbon, aromatic, and alogenic compounds. The differential effects of the strains were most likely due to the specific mixtures of mVOCs emitted by each strain, suggesting a synergistic effect occurs among the compounds present.

Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities

Bacterial communities are taxonomically highly diverse, yet the mechanisms that maintain this diversity remain poorly understood. We hypothesized that an obligate and mutual exchange of metabolites, as is very common among bacterial cells, could stabilize different genotypes within microbial communities. To test this, we developed a cellular automaton to model interactions among six empirically characterized genotypes that differ in their ability and propensity to produce amino acids. By systematically varying intrinsic (i.e. benefit-to-cost ratio) and extrinsic parameters (i.e. metabolite diffusion level, environmental amino acid availability), we show that obligate cross-feeding of essential metabolites is selected for under a broad range of conditions. In spatially structured environments, positive assortment among cross-feeders resulted in the formation of cooperative clusters, which limited exploitation by non-producing auxotrophs, yet allowed them to persist at the clusters' periphery. Strikingly, cross-feeding helped to maintain genotypic diversity within populations, while amino acid supplementation to the environment decoupled obligate interactions and favored auxotrophic cells that saved amino acid production costs over metabolically autonomous prototrophs. Together, our results suggest that spatially structured environments and limited nutrient availabilities should facilitate the evolution of metabolic interactions, which can help to maintain genotypic diversity within natural microbial populations.

Removal of methyl acrylate by ceramic-packed biotrickling filter and their response to bacterial community

Methyl acrylate is a widely used raw chemical materials and it is toxic in humans. In order to treat the methyl acrylate waste gas, a 3-layer BTF packed with ceramic particles and immobilized with activated sludge was set up. The BTF exhibited excellent removal efficiency that no methyl acrylate could be detected when EBRT was larger than 266s and inlet concentration was lower than 0.19g/m(3). The 1st layer performed the best at fixed inlet concentration of 0.42g/m(3). PCR combined with DGGE was performed to detect the differences in different layers of the BTF. Phylum Proteobacteria (e.g. α-, β-, γ-, δ-) was predominantly represented in the bacterial community, followed by Actinobacteria and Firmicutes. Desulfovibrio gigas, Variovorax paradoxus, Dokdonella koreensis, Pseudoxanthomonas suwonensis, Azorhizobium caulinodans, Hyphomicrobium denitrificans, Hyphomicrobium sp. and Comamonas testosteroni formed the bacteria community to treat methyl acrylate waste gas in the BTF.

The effect of oil spills on the bacterial diversity and catabolic function in coastal sediments: a case study on the Prestige oil spill

The accident of the Prestige oil tanker in 2002 contaminated approximately 900 km of the coastline along the northern Spanish shore, as well as parts of Portugal and France coast, with a mixture of heavy crude oil consisting of polycyclic aromatic hydrocarbons, alkanes, asphaltenes and resins. The capacity of the autochthonous bacterial communities to respond to the oil spill was assessed indirectly by determining the hydrocarbon profiles of weathered oil samples collected along the shore, as well as through isotope ratios of seawater-dissolved CO2, and directly by analyses of denaturing gradient gel electrophoresis fingerprints and 16S rRNA gene libraries. Overall, the results evidenced biodegradation of crude oil components mediated by natural bacterial communities, with a bias towards lighter and less substituted compounds. The changes observed in the Proteobacteria, the most abundant phylum in marine sediments, were related to the metabolic profiles of the sediment. The presence of crude oil in the supratidal and intertidal zones increased the abundance of Alpha- and Gammaproteobacteria, dominated by the groups Sphingomonadaceae, Rhodobacteraceae and Chromatiales, whilst Gamma- and Deltaproteobacteria were more relevant in subtidal zones. The phylum Actinobacteria, and particularly the genus Rhodococcus, was a key player in the microbial response to the spill, especially in the degradation of the alkane fraction. The addition of inorganic fertilizers enhanced total biodegradation rates, suggesting that, in these environments, nutrients were insufficient to support significant growth after the huge increase in carbon sources, as evidenced in other spills. The presence of bacterial communities able to respond to a massive oil input in this area was consistent with the important history of pollution of the region by crude oil.

Molecular Phylogenetic Diversity and Spatial Distribution of Bacterial Communities in Cooling Stage during Swine Manure Composting

Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and subsequent sub-cloning and sequencing were used in this study to analyze the molecular phylogenetic diversity and spatial distribution of bacterial communities in different spatial locations during the cooling stage of composted swine manure. Total microbial DNA was extracted, and bacterial near full-length 16S rRNA genes were subsequently amplified, cloned, RFLP-screened, and sequenced. A total of 420 positive clones were classified by RFLP and near-full-length 16S rDNA sequences. Approximately 48 operational taxonomic units (OTUs) were found among 139 positive clones from the superstratum sample; 26 among 149 were from the middle-level sample and 35 among 132 were from the substrate sample. Thermobifida fusca was common in the superstratum layer of the pile. Some Bacillus spp. were remarkable in the middle-level layer, and Clostridium sp. was dominant in the substrate layer. Among 109 OTUs, 99 displayed homology with those in the GenBank database. Ten OTUs were not closely related to any known species. The superstratum sample had the highest microbial diversity, and different and distinct bacterial communities were detected in the three different layers. This study demonstrated the spatial characteristics of the microbial community distribution in the cooling stage of swine manure compost.

Rhizosphere microbial community composition affects cadmium and zinc uptake by the metal-hyperaccumulating plant Arabidopsis halleri

The remediation of metal-contaminated soils by phytoextraction depends on plant growth and plant metal accessibility. Soil microorganisms can affect the accumulation of metals by plants either by directly or indirectly stimulating plant growth and activity or by (im)mobilizing and/or complexing metals. Understanding the intricate interplay of metal-accumulating plants with their rhizosphere microbiome is an important step toward the application and optimization of phytoremediation. We compared the effects of a "native" and a strongly disturbed (gamma-irradiated) soil microbial communities on cadmium and zinc accumulation by the plant Arabidopsis halleri in soil microcosm experiments. A. halleri accumulated 100% more cadmium and 15% more zinc when grown on the untreated than on the gamma-irradiated soil. Gamma irradiation affected neither plant growth nor the 1 M HCl-extractable metal content of the soil. However, it strongly altered the soil microbial community composition and overall cell numbers. Pyrosequencing of 16S rRNA gene amplicons of DNA extracted from rhizosphere samples of A. halleri identified microbial taxa (Lysobacter, Streptomyces, Agromyces, Nitrospira, "Candidatus Chloracidobacterium") of higher relative sequence abundance in the rhizospheres of A. halleri plants grown on untreated than on gamma-irradiated soil, leading to hypotheses on their potential effect on plant metal uptake. However, further experimental evidence is required, and wherefore we discuss different mechanisms of interaction of A. halleri with its rhizosphere microbiome that might have directly or indirectly affected plant metal accumulation. Deciphering the complex interactions between A. halleri and individual microbial taxa will help to further develop soil metal phytoextraction as an efficient and sustainable remediation strategy.

Polar front associated variation in prokaryotic community structure in Arctic shelf seafloor

Spatial variations in composition of marine microbial communities and its causes have largely been disclosed in studies comprising rather large environmental and spatial differences. In the present study, we explored if a moderate but temporally permanent climatic division within a contiguous arctic shelf seafloor was traceable in the diversity patterns of its bacterial and archaeal communities. Soft bottom sediment samples were collected at 10 geographical locations, spanning spatial distances of up to 640 km, transecting the oceanic polar front in the Barents Sea. The northern sampling sites were generally colder, less saline, shallower, and showed higher concentrations of freshly sedimented phytopigments compared to the southern study locations. Sampling sites depicted low variation in relative abundances of taxa at class level, with persistent numerical dominance by lineages of Gamma- and Deltaproteobacteria (57-66% of bacterial sequence reads). The Archaea, which constituted 0.7-1.8% of 16S rRNA gene copy numbers in the sediment, were overwhelmingly (85.8%) affiliated with the Thaumarchaeota. Beta-diversity analyses showed the environmental variations throughout the sampling range to have a stronger impact on the structuring of both the bacterial and archaeal communities than spatial effects. While bacterial communities were significantly influenced by the combined effect of several weakly selective environmental differences, including temperature, archaeal communities appeared to be more uniquely structured by the level of freshly sedimented phytopigments.