Genome sequences for six Rhodanobacter strains, isolated from soils and the terrestrial subsurface, with variable denitrification capabilities

Soil Bacterial Diversity Responds to Long-Term Establishment of Perennial Legumes in Warm-Season Grassland at Two Soil Depths

The introduction of rhizoma peanut (RP Arachis glabrata Benth) into bahiagrass (Paspalum notatum Flüggé) may require time to develop stable plant-soil microbe interactions as the microbial legacy of the previous plant community may be long-lasting. A previous study showed that <2 years of introducing rhizoma peanut into bahiagrass pastures minimally affected soil bacterial diversity and community composition. In this study, we compared the effects of the long-term inclusion of rhizoma peanut (>8 years) into bahiagrass on soil bacterial diversity and community composition against their monocultures at 0 to 15 and 15 to 30 cm soil depths using next-generation sequencing to target bacterial 16S V3-V4 regions. We observed that a well-established RP-bahiagrass mixed stand led to a 36% increase in bacterial alpha diversity compared to the bahiagrass monoculture. There was a shift from a soil bacterial community dominated by Proteobacteria (~26%) reported in other bahiagrass and rhizoma peanut studies to a soil bacterial community dominated by Firmicutes (39%) in our study. The relative abundance of the bacterial genus Crossiella, known for its antimicrobial traits, was enhanced in the presence of RP. Differences in soil bacterial diversity and community composition were substantial between 0 to 15 and 15 to 30 cm soil layers, with N2-fixing bacteria belonging to the phylum Proteobacteria concentrated in 0 to 15 cm. Introducing RP into bahiagrass pastures is a highly sustainable alternative to mineral N fertilizer inputs. Our results provide evidence that this system also promotes greater soil microbial diversity and is associated with unique taxa that require further study to better understand their contributions to healthy pastures.

Rhizosphere microbial community structure differs between constant subzero and freeze-thaw temperature regimes in a subarctic soil

In the Arctic and subarctic, climate change is causing reduced snowpack extent and earlier snowmelt. Shallower snowpack decreases the thermal insulation of underlying soil and results in more freeze-thaw conditions reflective of dynamic air temperatures. The aim of this study was to determine the effect of alternative temperature regimes on overall microbial community structure and rhizosphere recruitment across representatives of three subarctic plant functional groups. We hypothesized that temperature regime would influence rhizosphere community structure more than plant type. Planted microcosms were established using a tree, forb, grass, or no plant control and subjected to either freeze-thaw cycling or static subzero temperatures. Our results showed rhizosphere communities exhibited reduced diversity compared to bulk soils, and were influenced by temperature conditions and to a lesser extent plant type. We found that plants have a core microbiome that is persistent under different winter temperature scenarios but also have temperature regime-specific rhizosphere microbes. Freeze-thaw cycling resulted in greater community shifts from the pre-incubation soils when compared to constant subzero temperature. This finding suggests that wintertime snowpack conditions may be a significant factor for plant-microbe interactions upon spring thaw.

Agronomic strategies to enhance the early vigor and yield of maize. Part I: the role of seed applied biostimulant, hybrid and starter fertilization on rhizosphere bacteria profile and diversity

The sustainable intensification of maize-based systems may reduce greenhouse-gas emissions and the excessive use of non-renewable inputs. Considering the key role that the microbiological fertility has on crop growth and resilience, it is worth of interest studying the role of cropping system on the rhizosphere bacterial communities, that affect soil health and biological soil fertility. In this work we monitored and characterized the diversity and composition of native rhizosphere bacterial communities during the early growth phases of two maize genotypes of different early vigor, using a nitrogen (N)-phosphorus (P) starter fertilization and a biostimulant seed treatment, in a growth chamber experiment, by polymerase chain reaction-denaturing gradient gel electrophoresis of partial 16S rRNA gene and amplicon sequencing. Cluster analyses showed that the biostimulant treatment affected the rhizosphere bacterial microbiota of the ordinary hybrid more than that of the early vigor, both at plant emergence and at the 5-leaf stage. Moreover, the diversity indices calculated from the community profiles, revealed significant effects of NP fertilization on richness and the estimated effective number of species (H2) in both maize genotypes, while the biostimulant had a positive effect on plant growth promoting community of the ordinary hybrid, both at the plant emergence and at the fifth leaf stage. Our data showed that maize genotype was the major factor shaping rhizosphere bacterial community composition suggesting that the root system of the two maize hybrids recruited a different microbiota. Moreover, for the first time, we identified at the species and genus level the predominant native bacteria associated with two maize hybrids differing for vigor. These results pave the way for further studies to be performed on the effects of cropping system and specific crop practices, considering also the application of biostimulants, on beneficial rhizosphere microorganisms.

Temporal Changes in the Skin Microbiome of Epidermolysis Bullosa Patients following the Application of Wound Dressings

OBJECTIVE

Epidermolysis bullosa (EB) is a group of rare hereditary skin disorders characterized by the formation of painful blisters, erosions, and ulcers. In addition, the wounds can easily become infected with different pathogens. Therefore, the dynamics in the microbial populations across the various stages of EB can shed light on pathophysiology, the effect of treatment, and the factors involved in its recovery, but they are understudied. We thus sought to characterize the skin microbiome among patients with EB over time.

METHODS

A prospective study conducted in the pediatric dermatology clinic at Soroka Medical Center, Beer-Sheva, Israel. Children (0-18) with simplex and recessive dystrophic EB were sampled at two different time points: before a therapeutic regimen and 90 days (±14 days) later. Samples were obtained from lesional skin (wound), healthy, non-lesional skin, and seborrheic skin (forehead). Samples were subject to 16S rRNA amplicon sequencing. Analyses performed included comparisons of relative abundance at the phyla and genera taxonomic levels, alpha and beta diversity comparisons, and differential abundance.

RESULTS

32 children with EB were enrolled, for whom 192 skin microbiome samples were obtained. Lesional skin samples harbored significantly less Bacteroidota and Fusobacteriota before the initiation of treatment. Following topical dressing, we observed more Firmicutes and less Proteobacteria in lesional skin samples than healthy and seborrheic skin samples. In addition, Staphylococcus was significantly more abundant in lesional samples than in non-lesional and seborrheic samples following treatment.

CONCLUSIONS

Our study recaptured the reduced bacterial diversity and increased staphylococcal carriage in EB patients, showing a potential effect of topical dressing either directly on the wound microbiome or indirectly through the contribution towards skin healing. The detection of Firmicutes in general, and S. aureus specifically, commensurate with the application of a wound dressing may warrant the use of additional treatment methods to facilitate wound healing. Future studies in these patients should prospectively correlate the temporal changes in the microbiome associated with various treatment modalities in order to optimize the care of EB patients.

Effects of tea oil camellia (Camellia oleifera Abel.) shell-based organic fertilizers on the physicochemical property and microbial community structure of the rhizosphere soil

Soil microorganisms play important roles in promoting soil ecosystem restoration, but much of the current research has been limited to changes in microbial community structure in general, and little is known regarding the soil physicochemical property and microbial community structure. In this study, four organic fertilizers were first prepared based on tea oil camellia shell (TOCS). Our findings indicate that the application of BOFvo increased both total pore volume and BET surface area of the rhizosphere soils, as well there was a remarkable enhancement in total organic matter (TOM), total nitrogen (TN), available nitrogen (AN), total phosphorus (TP), total potassium (TK), and available potassium (AK) contents of the rhizosphere soils. Meanwhile, in comparison to the CK and CF groups, the utilization of BOFvo led to a substantial increase in both average yield and fruiting rate per plant at maturity, as well resulted in a significant increase in TN and TP contents of tea oil camellia leaves. Furthermore, our findings suggest that the application of TOCS-based organic fertilizers significantly enhances the microbial diversity in the rhizosphere soils with Proteobacteria and Ascomycota being the dominant bacterial and fungal phyla, respectively, and Rhodanobacter and Fusarium being the dominant bacterial and fungal genus, respectively. Redundancy analysis (RDA) indicates that the physicochemical characteristics of TOCS-based organic fertilizers had a significant impact on the composition and distribution of microbial communities in the rhizosphere soils. This study will facilitate the promotion and application of TOCS-based organic fertilizers, thereby establishing a foundation for the reuse of tea oil camellia waste resources.

Different Distribution of Core Microbiota in Upper Soil Layer in Two Places of North China Plain

Backgrounds:

Soils harbor diverse bacteria, and these bacteria play important roles in soil nutrition cycling and carbon storage. Numerous investigations of soil microbiota had been performed, and the core microbiota in different soil or vegetation soil types had been described. The upper layer of soil, as a source of organic matter, is important and affected by the habitats and dominant bacteria. However, the complexity of soil environments and relatively limited information of many geographic areas had attracted great attention on comprehensive exploration of soil microbes in enormous types of soil.

Methods:

To reveal the core upper layer soil microbiota, soil samples from metropolis and countryside regions in the North China Plain were investigated using high-throughput sequencing strategy.

Results:

The results showed that the most dominant bacteria are Proteobacteria (38.34%), Actinobacteria (20.56%), and Acidobacteria (15.18%). At the genus-level, the most abundant known genera are Gaiella (3.66%), Sphingomonas (3.6%), Acidobacteria Gp6 (3.52%), and Nocardioides (2.1%). Moreover, several dominant operational taxanomy units OTUs, such as OTU_3 and OTU_17, were identified to be associated with the soil environment. Microbial distributions of the metropolis samples were different from the countryside samples, which may reflect the environments in the countryside were more diverse than in the metropolis. Microbial diversity and evenness were higher in the metropolis than in the countryside, which might due to the fact that human activity increased the microbial diversity in the metropolis.

Conclusion:

The upper layer soil core microbiota of the North China Plain were complex, and microbial distributions in these two places might be mainly affected by the human activity and environmental factors, not by the distance. Our data highlights the upper layer soil core microbiota in North China Plain, and provides insights for future soil microbial distribution studies in central China.

Cross-kingdom interactions and functional patterns of active microbiota matter in governing deadwood decay

Microbial community members are the primary microbial colonizers and active decomposers of deadwood. This study placed sterilized standardized beech and spruce sapwood specimens on the forest ground of 8 beech- and 8 spruce-dominated forest sites. After 370 days, specimens were assessed for mass loss, nitrogen (N) content and ¹⁵N isotopic signature, hydrolytic and lignin-modifying enzyme activities. Each specimen was incubated with bromodeoxyuridine (BrdU) to label metabolically active fungal and bacterial community members, which were assessed using amplicon sequencing. Fungal saprotrophs colonized the deadwood accompanied by a distinct bacterial community that was capable of cellulose degradation, aromatic depolymerization, and N₂ fixation. The latter were governed by the genus Sphingomonas, which was co-present with the majority of saprotrophic fungi regardless of whether beech or spruce specimens were decayed. Moreover, the richness of the diazotrophic Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group was significantly correlated with mass loss, N content and ¹⁵N isotopic signature. By contrast, presence of obligate predator Bdellovibrio spp. shifted bacterial community composition and were linked to decreased beech deadwood decay rates. Our study provides the first account of the composition and function of metabolically active wood-colonizing bacterial and fungal communities, highlighting cross-kingdom interactions during the early and intermediate stages of wood decay.

Two-Dimensional Cell Separation: a High-Throughput Approach to Enhance the Culturability of Bacterial Cells from Environmental Samples

Culture-independent sequence data from various environmental samples have revealed an immense microbial diversity of environmental, clinical, and industrial importance that has not yet been cultured. Cultivation is imperative to validate findings emerging from cultivation-independent molecular data and exploit the isolated organisms for biotechnological purposes. Efforts have been made to boost the cultivability of microbes from environmental samples by use of a range of techniques and instrumentation. The manuscript presents a novel yet simple and innovative approach to improving the cultivability of natural microorganisms without sophisticated instrumentation. By employing gradient centrifugation combined with serial dilution (“two-dimensional cell separation”), significantly higher numbers of genera (>2-fold higher) and species (>3-fold higher) were isolated from environmental samples, including soil, anaerobic sludge, and landfill leachate, than from using serial dilution alone. This simple and robust protocol can be modified for any environment and culture medium and provides access to untapped microbial diversity.

IMPORTANCE In the manuscript, we have developed a novel yet simple and innovative approach to improving the cultivability of natural microorganisms without sophisticated instrumentation. The method used gradient centrifugation combined with serial dilution (two-dimensional cell separation) to improve taxum recovery from samples. This simple and robust protocol can be modified for any environment and culture medium and provides access to untapped microbial diversity. This approach can be incorporated with less labor and complexity in laboratories with minimal instrumentation. As cultivation is a workflow that is well suited to lower-resource microbiology labs, we believe improvements in cultivability can increase opportunities for scientific collaborations between low-resource labs and groups focused on high-resource cultivation-independent methodologies.

Variation in Bacterial Community Structure Under Long-Term Fertilization, Tillage, and Cover Cropping in Continuous Cotton Production

Agricultural practices alter the structure and functions of soil microbial community. However, few studies have documented the alterations of bacterial communities in soils under long-term conservation management practices for continuous crop production. In this study, we evaluated soil bacterial diversity using 16S rRNA gene sequencing and soil physical and chemical properties within 12 combinations of inorganic N fertilization, cover cropping, and tillage throughout a cotton production cycle. Soil was collected from field plots of the West Tennessee Agriculture Research and Education Center in Jackson, TN, United States. The site has been under continuous cotton production for 38 years. A total of 38,038 OTUs were detected across 171 soil samples. The dominant bacterial phyla were Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi, accounting for ∼70% of the total bacterial community membership. Conventional tillage increased alpha diversity in soil samples collected in different stages of cotton production. The effects of inorganic N fertilization and conventional tillage on the structure of bacterial communities were significant at all four sampling dates (p < 0.01). However, cover cropping (p < 0.05) and soil moisture content (p < 0.05) only showed significant influence on the bacterial community structure after burn-down of the cover crops and before planting of cotton (May). Nitrate-N appeared to have a significant effect on the structure of bacterial communities after inorganic fertilization and at the peak of cotton growth (p < 0.01). Structural equation modeling revealed that the relative abundances of denitrifying and nitrifying bacteria were higher when conventional tillage and vetch cover crop practices were applied, respectively. Our results indicate that long-term tillage and fertilization are key factors increasing the diversity and restructuring the composition of bacterial communities, whereas cover cropping may have shorter-term effects on soil bacteria community structure. In this study, management practices might positively influence relative abundances of bacterial functional groups associated with N cycling. The bacteria functional groups may build a network for providing N and meet microbial N needs in the long term.

Seaweed Fertilizer Prepared by EM-Fermentation Increases Abundance of Beneficial Soil Microbiome in Paddy (Oryza sativa L.) during Vegetative Stage

Excessive use of chemical fertilizer could potentially decrease soil productivity by decreasing soil microbiome diversity. In this study, we evaluated the effects of fermented seaweed fertilizer in the soil microbial community of paddy plants (Oryza sativa L.). The paddy seedlings were divided into five groups, control (C0), chemical fertilizer (CF), seaweed fertilizer (SF), chemical and seaweed fertilizer combination 50:50 (CFSF1), and chemical and fertilizer combination 75:25 (CFSF2). The CFSF1 combination showed to be the most effective in inducing plant height (83.99 ± 3.70 cm) and number of tillers (24.20 ± 4.08). After 8 weeks after transplantation, the isolated DNA from each soil treatment were subjected to 16S rRNA (v3–v4 region) next-generation sequencing. The beneficial Acidobacteriota was most abundant in CFSF1. At genus level, the nitrifying bacteria MND1 was seen to be abundant in CFSF1 and also present in other SF treatments. The genus Chujaibacter is highly abundant in CF, which potentially plays a role in denitrification resulting in soil degradation. In addition, the CFSF1-treated soils show significantly higher diversity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). The current results could potentially contribute to the utilization of SF as a bioremediator and promoting green agriculture practice by reducing the amount of CF usage.

Bacterial communities in the rhizosphere of biofortified BRS pontal and conventional carioca bean (Phaseolus vulgaris) plants

The current knowledge of bean plants microbiome is far from being complete. Unraveling the complexity of the bacterial communities within common bean cultivars that may significantly contribute to plant health, growth and protection against soil pathogens, represents a major challenge. In this study, the richness and composition of the bacterial communities from bean plant rhizospheres and control bulk soils were analyzed by high-throughput sequencing and comparative analyses. From the classified sequences, Proteobacteria represented the most abundant phylum (42-66%), followed by Acidobacteria (12-36%) and Actinobacteria (11-18%), Bacterial community structures were different between bulk soil and rhizosphere samples. Comparing the bean cultivars, the biofortified cultivar presented high number of sequences affiliated to the genera Burkholderia and Rhodanobacter. Interestingly, despite the presence of stable and persistent core bacterial taxa associated with the common bean varieties, our analysis suggested that the biofortified common bean cultivar could select and maintain differential abundances of microbial groups in the rhizosphere environment.

Diversity of microbial communities and genes involved in nitrous oxide emissions in Antarctic soils impacted by marine animals as revealed by metagenomics and 100 metagenome-assembled genomes

Antarctic soils generally have low temperatures and limited availability of liquid water and nutrients. However, animals can increase the nutrient availability of ice-free areas by transferring nutrients from marine to terrestrial ecosystems, mainly through their excreta. In this study, we employed shotgun metagenomics and population genome binning techniques to study the diversity of microbial communities in Antarctic soils impacted by marine pinnipeds and birds relative to soils with no evident animal presence. We obtained ~285,000 16S rRNA gene-carrying metagenomic reads representing ~60 phyla and 100 metagenome-assembled genomes (MAGs) representing eight phyla. Only nine of these 100 MAGs represented previously described species, revealing that these soils harbor extensive novel diversity. Proteobacteria, Actinobacteria, and Bacteroidetes were the most abundant phyla in all samples, with Rhodanobacter being one of the most abundant genera in the bird-impacted soils. Further, the relative abundance of genes related to denitrification was at least double in soils impacted by birds than soils without animal influence. These results advance our understanding of the microbial populations and their genes involved in nitrous oxide emissions in ice-free coastal Antarctic soils impacted by marine animals and reveal novel microbial diversity associated with these ecosystems.

Ecotoxicological effects of copper oxide nanoparticles (nCuO) on the soil microbial community in a biosolids-amended soil

This study represents a holistic approach in assessing the effects of copper oxide nanoparticles (nCuO) on microbial health and community structure in soil amended with municipal biosolids. The biosolids were amended with nCuO (<50 nm) and mixed into a sandy loam soil at measured Cu concentrations of 27, 54, 123, 265 and 627 mg Cu kg^-1 soil. A suite of tests were used to assess the potential impact of nCuO on microbial growth, activity, and diversity. Microbial growth was determined by the heterotrophic plate count (HPC) method, while microbial diversity was assessed using both community level physiological profiling (CLPP) and 16S ribosomal DNA (rDNA) sequencing. Microbial activity was assessed by examining soil nitrification, organic matter decomposition, soil respiration (basal and substrate induced) and soil enzyme assays for dehydrogenase, phosphatase and β-glucosidase activities. As a readily soluble positive control, copper sulfate (CuSO₄) was used at measured Cu concentrations of 65, 140, 335 and 885 mg Cu kg^-1 soil for select tests, and at the highest concentration for the remaining tests. Analysis on Cu bioavailability revealed that extractable Cu²⁺ was higher in CuSO₄-spiked soils than nCuO-spiked soils. At a nCuO exposure concentration of ≤265 mg Cu kg^-1 soil, stimulatory effects were observed in nitrification, β-glucosidase and community level physiological profiling (CLPP) tests. nCuO showed no significant inhibitory effects on the soil microbial growth, activity or diversity at the highest concentration (i.e. 627 mg Cu kg^-1 soil), with the exception of the dehydrogenase (i.e. ≥27 mg Cu kg^-1 soil) and phosphatase (i.e. 627 mg Cu kg^-1 soil) enzyme activities. In contrast, inhibition from CuSO₄ at 885 mg Cu kg^-1 soil was observed in all tests with the exception of β-glucosidase enzyme activity. The growth of a Cu tolerant bacterium, Rhodanobacter sp., was observed at 885 mg Cu kg^-1 soil (CuSO₄).

Lettuce (Lactuca sativa) productivity influenced by microbial inocula under nitrogen-limited conditions in aquaponics

The demand for food will outpace productivity of conventional agriculture due to projected growth of the human population, concomitant with shrinkage of arable land, increasing scarcity of freshwater, and a rapidly changing climate. While aquaponics has potential to sustainably supplement food production with minimal environmental impact, there is a need to better characterize the complex interplay between the various components (fish, plant, microbiome) of these systems to optimize scale up and productivity. Here, we investigated how the commonly-implemented practice of continued microbial community transfer from pre-existing systems might promote or impede productivity of aquaponics. Specifically, we monitored plant growth phenotypes, water chemistry, and microbiome composition of rhizospheres, biofilters, and fish feces over 61-days of lettuce (Lactuca sativa var. crispa) growth in nitrogen-limited aquaponic systems inoculated with bacteria that were either commercially sourced or originating from a pre-existing aquaponic system. Lettuce above- and below-ground growth were significantly reduced across replicates treated with a pre-existing aquaponic system inoculum when compared to replicates treated with a commercial inoculum. Reduced productivity was associated with enrichment in specific bacterial genera in plant roots, including Pseudomonas, following inoculum transfer from pre-existing systems. Increased productivity was associated with enrichment of nitrogen-fixing Rahnella in roots of plants treated with the commercial inoculum. Thus, we show that inoculation from a pre-existing system, rather than from a commercial inoculum, is associated with lower yields. Further work will be necessary to test the putative mechanisms involved.

Alternation of soil bacterial and fungal communities by tomato-rice rotation in Hainan Island in Southeast of China

Tomato-rice rotation is prevalent in subtropical and tropical regions in China. This practice enhances crop productivity and the disease suppression property of soils against soil-borne plant pathogens. To explore the variations and dynamics of bacterial and fungal communities, bulk soil samples were collected during two consecutive years under a rotation system between tomato and rice originated from the year of 2010 in Hainan Island, and 16S rDNA and ITS amplicons were sequenced by Illumina MiSeq. The results demonstrated that potentially beneficial bacterial phyla Acidobacteria, Chloroflexi and genus Paenibacillus, as well as the fungal genus Mortierella were significantly enriched, while the potentially pathogenic fungal genus Fusarium was significantly decreased during the crop rotation. Measurements of soil physicochemical properties indicated that the soil acidification was improved. Redundancy analysis (RDA) revealed the correlation of the microbial community with soil pH and identified soil total phosphorus (TP) level as the highest determinant factor for both bacterial and fungal communities. This work provides a preliminary description of changes of the bacterial and fungal communities related to tomato-rice rotation in China and offered experimental evidences for exploring the effects of this agricultural practice on soil ecology.

Enrichment of Comammox and Nitrite-Oxidizing Nitrospira From Acidic Soils

In agricultural soils fertilized with a high amount of ammonium nitrogen, the pH decreases because of the oxidation of ammonia by nitrifiers. Molecular-based analyses have revealed that members of the genus Nitrospira dominate over other nitrifiers in some acidic soils. However, terrestrial Nitrospira are rarely cultivated and little is known about their ecophysiology. In addition, recent studies discovered a single microbe with the potential to oxidize both ammonia and nitrite (complete ammonia oxidizer; comammox) within Nitrospira, which had been previously recognized as a nitrite oxidizer. Despite their broad distribution, there are no enrichment samples of comammox from terrestrial or acidic environments. Here, we report the selective enrichment of both comammox and nitrite-oxidizing Nitrospira from the acidic soil of a heavily fertilized tea field. Long-term enrichment was performed with two individual continuous-feeding bioreactors capable of controlling ammonia or nitrite concentration and pH. We found that excessive ammonium supply was a key factor to enhance the growth of comammox Nitrospira under acidic conditions. Additionally, a low concentration of nitrite was fed to prevent the accumulation of free nitrous acid and inhibition of cell growth under low pH, resulting in the selective enrichment of nitrite-oxidizing Nitrospira. Based on 16S rRNA gene analysis, Nitrospira accounting for only 1.2% in an initial soil increased to approximately 80% of the total microorganisms in both ammonia- and nitrite-fed bioreactors. Furthermore, amoA amplicon sequencing revealed that two phylotypes belonging to comammox clade A were enriched in an ammonia-fed bioreactor. One group was closely related to previously cultivated strains, and the other was classified into a different cluster consisting of only uncultivated representatives. These two groups coexisted in the bioreactor controlled at pH 6.0, but the latter became dominant after the pH decreased to 5.5. Additionally, a physiological experiment revealed that the enrichment sample oxidizes ammonia at pH <4, which is in accordance with the strongly acidic tea field soil; this value is lower than the active pH range of isolated acid-adapted nitrifiers. In conclusion, we successfully enriched multiple phylotypes of comammox and nitrite-oxidizing Nitrospira and revealed that the pH and concentrations of protonated N-compounds were potential niche determinants.

Characterization of Bacterial and Fungal Assemblages From Historically Contaminated Metalliferous Soils Using Metagenomics Coupled With Diffusion Chambers and Microbial Traps

The majority of environmental microbiomes are not amenable to cultivation under standard laboratory growth conditions and hence remain uncharacterized. For environmental applications, such as bioremediation, it is necessary to isolate microbes performing the desired function, which may not necessarily be the fast growing or the copiotroph microbiota. Toward this end, cultivation and isolation of microbial strains using diffusion chambers (DC) and/or microbial traps (MT) have both been recently demonstrated to be effective strategies because microbial enrichment is facilitated by soil nutrients and not by synthetically defined media, thus simulating their native habitat. In this study, DC/MT chambers were established using soils collected from two US Department of Energy (DOE) sites with long-term history of heavy metal contamination, including mercury (Hg). To characterize the contamination levels and nutrient status, soils were first analyzed for total mercury (THg), methylmercury (MeHg), total carbon (TC), total nitrogen (TN), and total phosphorus (TP). Multivariate statistical analysis on these measurements facilitated binning of soils under high, medium and low levels of contamination. Bacterial and fungal microbiomes that developed within the DC and MT chambers were evaluated using comparative metagenomics, revealing Chthoniobacter, Burkholderia and Bradyrhizobium spp., as the predominant bacteria while Penicillium, Thielavia, and Trichoderma predominated among fungi. Many of these core microbiomes were also retrieved as axenic isolates. Furthermore, canonical correspondence analysis (CCA) of biogeochemical measurements, metal concentrations and bacterial communities revealed a positive correlation of Chthoniobacter/Bradyrhizobium spp., to THg whereas Burkholderia spp., correlated with MeHg. Penicillium spp., correlated with THg whereas Trichoderma spp., and Aspergillus spp., correlated with MeHg, from the MT approach. This is the first metagenomics-based assessment, isolation and characterization of soil-borne bacterial and fungal communities colonizing the diffusion chambers (DC) and microbial traps (MT) established with long-term metal contaminated soils. Overall, this study provides proof-of-concept for the successful application of DC/MT based assessment of mercury resistant (HgR) microbiomes in legacy metal-contaminated soils, having complex contamination issues. Overall, this study brings out the significance of microbial communities and their relevance in context to heavy metal cycling for better stewardship and restoration of such historically contaminated systems.

Microbiota in Waterlogged Archaeological Wood: Use of Next-Generation Sequencing to Evaluate the Risk of Biodegradation

Waterlogged archaeological wood (WAW) is considered a precious material, first-hand account of past civilizations. Like any organic material, it is subjected to biodegradative action of microorganisms whose activity could be particularly fast and dangerous during the phases of excavation, storage and restoration. The present work aimed to characterize the microorganisms present in WAW during these tricky periods to evaluate the biological risk it is exposed to. The bacterial and fungal communities inhabiting woods coming from two archaeological sites (Pisa and Naples) were investigated through Next-Generation Sequencing (NGS). High-throughput sequencing of extracted DNA fragments was performed using the reversible terminator-based sequencing chemistry with the Illumina MiSeq platform. The analyses revealed that the two archaeological sites showed distinct richness and biodiversity, as expected. In all the WAWs, the bacterial community harbored mainly Proteobacteria, whereas Bacteroidetes was well represented only in Naples communities and taxa belonging to the phyla Chloroflexi only in the Pisa site. Concerning the fungal community, the two sites were dominated by different phyla: Ascomycota for Naples samples and Basidiomycota for Pisa. Interestingly, most of the identified bacterial and fungal taxa have cellulolytic or ligninolytic ability. These results provide new and useful background information concerning the composition of WAW microbiota and the threat it represents for this precious material.

Insights into the Function and Horizontal Transfer of Isoproturon Degradation Genes (pdmAB) in a Biobed System

Biobeds, designed to minimize pesticide point source contamination, rely mainly on biodegradation processes. We studied the interactions of a biobed microbial community with the herbicide isoproturon (IPU) to explore the role of the pdmA gene, encoding the large subunit of an N-demethylase responsible for the initial demethylation of IPU, via quantitative PCR (qPCR) and reverse transcription-PCR (RT-qPCR) and the effect of IPU on the diversity of the total bacterial community and its active fraction through amplicon sequencing of DNA and RNA, respectively. We further investigated the localization and dispersal mechanisms of pdmAB in the biobed packing material by measuring the abundance of the plasmid pSH (harboring pdmAB) of the IPU-degrading Sphingomonas sp. strain SH (previously isolated from the soil used in the biobed) compared with the abundance of the pdmA gene and metagenomic fosmid library screening. pdmA abundance and expression increased concomitantly with IPU mineralization, verifying its major role in IPU transformation in the biobed system. DNA- and RNA-based 16S rRNA gene sequencing analysis showed no effects on bacterial diversity. The pdmAB-harboring plasmid pSH showed a consistently lower abundance than pdmA, suggesting the localization of pdmAB in replicons other than pSH. Metagenomic analysis identified four pdmAB-carrying fosmids. In three of these fosmids, the pdmAB genes were organized in a well-conserved operon carried by sphingomonad plasmids with low synteny with pSH, while the fourth fosmid contained an incomplete pdmAB cassette localized in a genomic fragment of a Rhodanobacter strain. Further analysis suggested a potentially crucial role of IS6 and IS256 in the transposition and activation of the pdmAB operon.IMPORTANCE Our study provides novel insights into the interactions of IPU with the bacterial community of biobed systems, reinforces the assumption of a transposable nature of IPU-degrading genes, and verifies that on-farm biobed systems are hot spots for the evolution of pesticide catabolic traits.

Growing-season length and soil microbes influence the performance of a generalist bunchgrass beyond its current range

As organisms shift their geographic distributions in response to climate change, biotic interactions have emerged as an important factor driving the rate and success of range expansions. Plant-microbe interactions are an understudied but potentially important factor governing plant range shifts. We studied the distribution and function of microbes present in high-elevation unvegetated soils, areas that plants are colonizing as climate warms, snow melts earlier, and the summer growing season lengthens. Using a manipulative snowpack and microbial inoculation transplant experiment, we tested the hypothesis that growing-season length and microbial community composition interact to control plant elevational range shifts. We predicted that a lengthening growing season combined with dispersal to patches of soils with more mutualistic microbes and fewer pathogenic microbes would facilitate plant survival and growth in previously unvegetated areas. We identified negative effects on survival of the common alpine bunchgrass Deschampsia cespitosa in both short and long growing seasons, suggesting an optimal growing-season length for plant survival in this system that balances time for growth with soil moisture levels. Importantly, growing-season length and microbes interacted to affect plant survival and growth, such that microbial community composition increased in importance in suboptimal growing-season lengths. Further, plants grown with microbes from unvegetated soils grew as well or better than plants grown with microbes from vegetated soils. These results suggest that the rate and spatial extent of plant colonization of unvegetated soils in mountainous areas experiencing climate change could depend on both growing-season length and soil microbial community composition, with microbes potentially playing more important roles as growing seasons lengthen.

Glutaredoxin-like protein (GLP)-a novel bacteria sulfurtransferase that protects cells against cyanide and oxidative stresses

The pathogen Xylella fastidiosa belongs to the Xanthomonadaceae family, a large group of Gram-negative bacteria that cause diseases in many economically important crops. A predicted gene, annotated as glutaredoxin-like protein (glp), was found to be highly conserved among the genomes of different genera within this family and highly expressed in X. fastidiosa. Analysis of the GLP protein sequences revealed three protein domains: one similar to monothiol glutaredoxins (Grx), an Fe-S cluster and a thiosulfate sulfurtransferase/rhodanese domain (Tst/Rho), which is generally involved in sulfur metabolism and cyanide detoxification. To characterize the biochemical properties of GLP, we expressed and purified the X. fastidiosa recombinant GLP enzyme. Grx activity and Fe-S cluster formation were not observed, while an evaluation of Tst/Rho enzymatic activity revealed that GLP can detoxify cyanide and transfer inorganic sulfur to acceptor molecules in vitro. The biological activity of GLP relies on the cysteine residues in the Grx and Tst/Rho domains (Cys³³ and Cys²⁶⁶, respectively), and structural analysis showed that GLP and GLP^C266S were able to form high molecular weight oligomers (> 600 kDa), while replacement of Cys³³ with Ser destabilized the quaternary structure. In vivo heterologous enzyme expression experiments in Escherichia coli revealed that GLP can protect bacteria against high concentrations of cyanide and hydrogen peroxide. Finally, phylogenetic analysis showed that homologous glp genes are distributed across Gram-negative bacterial families with conservation of the N- to C-domain order. However, no eukaryotic organism contains this enzyme. Altogether, these results suggest that GLP is an important enzyme with cyanide-decomposing and sulfurtransferase functions in bacteria, whose presence in eukaryotes we could not observe, representing a promising biological target for new pharmaceuticals.

Effect of Applying Struvite and Organic N as Recovered Fertilizers on the Rhizosphere Dynamics and Cultivation of Lupine (Lupinus angustifolius)

Intensive agriculture and horticulture heavily rely on the input of fertilizers to sustain food (and feed) production. However, high carbon footprint and pollution are associated with the mining processes of P and K, and the artificial nitrogen fixation for the production of synthetic fertilizers. Organic fertilizers or recovered nutrients from different waste sources can be used to reduce the environmental impact of fertilizers. We tested two recovered nutrients with slow-release patterns as promising alternatives for synthetic fertilizers: struvite and a commercially available organic fertilizer. Using these fertilizers as a nitrogen source, we conducted a rhizotron experiment to test their effect on plant performance and nutrient recovery in lupine plants. Plant performance was not affected by the fertilizer applied; however, N recovery was higher from the organic fertilizer than from struvite. As root architecture is fundamental for plant productivity, variations in root structure and length as a result of soil nutrient availability driven by plant-bacteria interactions were compared showing also no differences between fertilizers. However, fertilized plants were considerably different in the root length and morphology compared with the no fertilized plants. Since the microbial community influences plant nitrogen availability, we characterized the root-associated microbial community structure and functionality. Analyses revealed that the fertilizer applied had a significant impact on the associations and functionality of the bacteria inhabiting the growing medium used. The type of fertilizer significantly influenced the interindividual dissimilarities in the most abundant genera between treatments. This means that different plant species have a distinct effect on modulating the associated microbial community, but in the case of lupine, the fertilizer had a bigger effect than the plant itself. These novel insights on interactions between recovered fertilizers, plant, and associated microbes can contribute to developing sustainable crop production systems.

Odor removal by and microbial community in the enhanced landfill cover materials containing biochar-added sludge compost under different operating parameters

Odor problem has become a growing concern for municipal solid waste (MSW) operators and communities located close to landfill sites. In this study, nine laboratory-scale landfill reactors were used to simulate in-situ odor control by a novel landfill cover material consisting of biochar-added sludge compost under various operating parameters. Characterization of odor removal and microbial community in the cover layer under various operating parameters was conducted using gas chromatograph-mass spectrometry and 454 high-throughput pyrosequencing, respectively. Results showed that H₂S (76.9-86.0%) and volatile organic sulfur compounds (VOSCs) (12.3-21.7%) were dominant according to their theoretical generated odor concentrations. The total odor REs calculated using the theoretical odor concentrations in the landfill reactors were different than using the measured odor values, which were ranked from high to low as: R6 > R5 > R7 > R4 > R8 > R9 > R3 > R2 > R1, showing the largest discrepancy of 25.3%. The optimum combination of operating parameters based on the theoretical odor concentration was different with that based on the measured odor concentrations. Moreover, although Firmicutes (12.21-91.48%), Proteobacteria (3.55-51.03%), and Actinobacteria (4.01-47.39%) were in general the three major bacterial phyla found in the landfill covers, the detailed bacterial communities in the cover materials of the simulated reactors varied with various operating parameters. Alicyclobacillus and Tuberibacillus showed positive correlations with the removal efficiencies (REs) of chlorinated compounds, H₂S, aromatic compounds, volatile organic sulfur compounds (VOSCs), and organic acids. The correlations of Rhodanobacter, Gemmatimonas, Flavisolibacter and Sphingomonas were strongly positive with ammonia RE and relatively positive with REs of organic acids, VOSCs, and aromatic compounds. These findings are instrumental in understanding the relationship between the structure of microbial communities and odor removal performances, and in developing techniques for in-situ odor control at landfills.

Xylitol and sorbitol effects on the microbiome of saliva and plaque

Chewing gum containing xylitol may help prevent caries by reducing levels of mutans streptococci (MS) and lactobacilli in saliva and plaque. Very little is known about other species which are possibly beneficial to oral health. In this study, we employed high-throughput sequencing of the 16S rRNA gene to profile microbial communities of saliva and plaque following short-term consumption of xylitol and sorbitol containing chewing gum. Participants (n = 30) underwent a washout period and were randomly assigned to one of two groups. Each group chewed either xylitol or sorbitol gum for three weeks, before undergoing a second four-week washout period after which they switched to the alternate gum for three weeks. Analysis of samples collected before and after each intervention identified distinct plaque and saliva microbial communities that altered dependent on the order in which gum treatments were given. Neither the xylitol nor sorbitol treatments significantly affected the bacterial composition of plaque. Lactobacilli were undetected and the number of Streptococcus mutans sequence reads was very low and unaffected by either xylitol or sorbitol. However, sorbitol affected several other streptococcal species in saliva including increasing the abundance of S. cristatus, an oral commensal shown to inhibit bacteria associated with chronic periodontitis.

Concentration-dependent responses of soil bacterial, fungal and nitrifying communities to silver nano and micron particles

The growing use of silver nanoparticles (AgNPs) is likely to result in increased environmental contamination. Although AgNPs have been reported to affect microbial communities in a range of ecosystems, there is still a lack of information concerning the effect of low concentrations of AgNPs on soil microbial community structures and functional groups involved in biogeochemical cycling. In this study, the concentration-dependent effects of AgNPs and silver micron particles (AgMPs) on bacterial and fungal community structures in an agricultural pastureland soil were examined in a microcosm-based experiment using enzyme analysis, molecular fingerprinting, qPCR and amplicon sequencing. Soil enzyme processes were impacted by Ag contamination, with soil dehydrogenase activity reduced by 1 mg kg^-1 of AgNPs and AgMPs. Soil urease activity was less susceptible, but was inhibited by ≥ 10 mg kg^-1 AgNPs. The significant (P ≤ 0.001) decrease in copy numbers of the amoA gene by 10 mg kg^-1 AgNPs indicated that archaea ammonia oxidisers may be more sensitive to AgNP contamination than bacteria. Amplicon sequencing revealed the bacterial phyla Acidobacteria and Verrucomicrobia to be highly sensitive to AgNP contamination. A broad reduction in the relative abundance of Acidobacterial genera was observed, with the exception of the genus Geothrix which increased in response to AgNP and AgMP amendment. Broad tolerance to Ag was observed among the Bacteriodetes, with higher relative abundance of most genera observed in the presence of AgNPs and AgMPs. The proteobacterial genus Dyella was highly tolerant to AgNPs and AgMPs and relative abundance of this genus increased with Ag concentration. Soil fungal community structure responded to both AgNPs and AgMPs, but the nanoparticle had an impact at a lower concentration. This study demonstrates that pastureland soil microbial communities are highly sensitive to AgNP amendment and key functional processes may be disrupted by relatively low levels of contamination.

Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning

Contamination from anthropogenic activities has significantly impacted Earth’s biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN), representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate) increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not nitrate) increased in groundwater. In addition, about 5.9% of specific key functional populations targeted by a comprehensive functional gene array (GeoChip 5) increased significantly (P < 0.05) as uranium or nitrate increased, and their changes could be used to successfully predict uranium and nitrate contamination and ecosystem functioning. This study indicates great potential for using microbial functional genes to predict environmental contamination and ecosystem functioning.

Disentangling the relationships between biodiversity and ecosystem functioning is an important but poorly understood topic in ecology. Predicting ecosystem functioning on the basis of biodiversity is even more difficult, particularly with microbial biomarkers. As an exploratory effort, this study used key microbial functional genes as biomarkers to provide predictive understanding of environmental contamination and ecosystem functioning. The results indicated that the overall functional gene richness/diversity decreased as uranium increased in groundwater, while specific key microbial guilds increased significantly as uranium or nitrate increased. These key microbial functional genes could be used to successfully predict environmental contamination and ecosystem functioning. This study represents a significant advance in using functional gene markers to predict the spatial distribution of environmental contaminants and ecosystem functioning toward predictive microbial ecology, which is an ultimate goal of microbial ecology.

The Effects of Cropping Regimes on Fungal and Bacterial Communities of Wheat and Faba Bean in a Greenhouse Pot Experiment Differ between Plant Species and Compartment

Many bacteria and fungi in the plant rhizosphere and endosphere are beneficial to plant nutrient acquisition, health, and growth. Although playing essential roles in ecosystem functioning, our knowledge about the effects of multiple cropping regimes on the plant microbiome and their interactions is still limited. Here, we designed a pot experiment simulating different cropping regimes. For this purpose, wheat and faba bean plants were grown under controlled greenhouse conditions in monocultures and in two intercropping regimes: row and mixed intercropping. Bacterial and fungal communities in bulk and rhizosphere soils as well as in the roots and aerial plant parts were analyzed using large-scale metabarcoding. We detected differences in microbial richness and diversity between the cropping regimes. Generally, observed effects were attributed to differences between mixed and row intercropping or mixed intercropping and monoculture. Bacterial and fungal diversity were significantly higher in bulk soil samples of wheat and faba bean grown in mixed compared to row intercropping. Moreover, microbial communities varied between crop species and plant compartments resulting in different responses of these communities toward cropping regimes. Leaf endophytes were not affected by cropping regime but bacterial and fungal community structures in bulk and rhizosphere soil as well as fungal community structures in roots. We further recorded highly complex changes in microbial interactions. The number of negative inter-domain correlations between fungi and bacteria decreased in bulk and rhizosphere soil in intercropping regimes compared to monocultures due to beneficial effects. In addition, we observed plant species-dependent differences indicating that intra- and interspecific competition between plants had different effects on the plant species and thus on their associated microbial communities. To our knowledge, this is the first study investigating microbial communities in different plant compartments with respect to multiple cropping regimes using large-scale metabarcoding. Although a simple design simulating different cropping regimes was used, obtained results contribute to the understanding how cropping regimes affect bacterial and fungal communities and their interactions in different plant compartments. Nonetheless, we need field experiments to properly quantify observed effects in natural ecosystems.

Application of acclimated sewage sludge as a bio-augmentation/bio-stimulation strategy for remediating chlorpyrifos contamination in soil with/without cadmium

This experiment was performed to investigate the effects of acclimated sewage sludge (ASS) and sterilized ASS on the fates of chlorpyrifos (CP) in soil with or without cadmium (Cd), as well as the improvement of soil biochemical properties. Results showed that both ASS and sterilized ASS could significantly promote CP dissipation, and the groups with ASS had the highest efficiency on CP removal, whose degradation rates reached 71.3%-85.9% at the 30th day (40.4%-50.2% higher than non-sludge groups). Besides, the degradation rate of CP was not severely influenced by the existence of Cd, and the population of soil microorganism dramatically increased after adding sludge. The soil enzyme activities (dehydrogenase, acid phosphatase and FDA hydrolase activities) ranked from high to low were as follows: groups with sterilized ASS>groups with ASS>groups without sludge. Simultaneously, 16S rRNA gene sequencing revealed that ASS changed bacterial community structure and diversity in soil. In addition, alkali-hydrolyzable nitrogen and Olsen- phosphorus increased after application of sludge, indicating that the addition of ASS (or sterilized ASS) could effectively improve soil fertility.

Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community

Unraveling the drivers controlling the response and adaptation of biological communities to environmental change, especially anthropogenic activities, is a central but poorly understood issue in ecology and evolution. Comparative genomics studies suggest that lateral gene transfer (LGT) is a major force driving microbial genome evolution, but its role in the evolution of microbial communities remains elusive. To delineate the importance of LGT in mediating the response of a groundwater microbial community to heavy metal contamination, representative Rhodanobacter reference genomes were sequenced and compared to shotgun metagenome sequences. 16S rRNA gene-based amplicon sequence analysis indicated that Rhodanobacter populations were highly abundant in contaminated wells with low pHs and high levels of nitrate and heavy metals but remained rare in the uncontaminated wells. Sequence comparisons revealed that multiple geochemically important genes, including genes encoding Fe²⁺/Pb²⁺ permeases, most denitrification enzymes, and cytochrome c₅₅₃, were native to Rhodanobacter and not subjected to LGT. In contrast, the Rhodanobacter pangenome contained a recombinational hot spot in which numerous metal resistance genes were subjected to LGT and/or duplication. In particular, Co²⁺/Zn²⁺/Cd²⁺ efflux and mercuric resistance operon genes appeared to be highly mobile within Rhodanobacter populations. Evidence of multiple duplications of a mercuric resistance operon common to most Rhodanobacter strains was also observed. Collectively, our analyses indicated the importance of LGT during the evolution of groundwater microbial communities in response to heavy metal contamination, and a conceptual model was developed to display such adaptive evolutionary processes for explaining the extreme dominance of Rhodanobacter populations in the contaminated groundwater microbiome.

Lateral gene transfer (LGT), along with positive selection and gene duplication, are the three main mechanisms that drive adaptive evolution of microbial genomes and communities, but their relative importance is unclear. Some recent studies suggested that LGT is a major adaptive mechanism for microbial populations in response to changing environments, and hence, it could also be critical in shaping microbial community structure. However, direct evidence of LGT and its rates in extant natural microbial communities in response to changing environments is still lacking. Our results presented in this study provide explicit evidence that LGT played a crucial role in driving the evolution of a groundwater microbial community in response to extreme heavy metal contamination. It appears that acquisition of genes critical for survival, growth, and reproduction via LGT is the most rapid and effective way to enable microorganisms and associated microbial communities to quickly adapt to abrupt harsh environmental stresses.

Deconstructing the polymerase chain reaction: understanding and correcting bias associated with primer degeneracies and primer-template mismatches

The polymerase chain reaction (PCR) is sensitive to mismatches between primer and template, and mismatches can lead to inefficient amplification of targeted regions of DNA template. In PCRs in which a degenerate primer pool is employed, each primer can behave differently. Therefore, inefficiencies due to different primer melting temperatures within a degenerate primer pool, in addition to mismatches between primer binding sites and primers, can lead to a distortion of the true relative abundance of targets in the original DNA pool. A theoretical analysis indicated that a combination of primer-template and primer-amplicon interactions during PCR cycles 3–12 is potentially responsible for this distortion. To test this hypothesis, we developed a novel amplification strategy, entitled “Polymerase-exonuclease (PEX) PCR”, in which primer-template interactions and primer-amplicon interactions are separated. The PEX PCR method substantially and significantly improved the evenness of recovery of sequences from a mock community of known composition, and allowed for amplification of templates with introduced mismatches near the 3’ end of the primer annealing sites. When the PEX PCR method was applied to genomic DNA extracted from complex environmental samples, a significant shift in the observed microbial community was detected. Furthermore, the PEX PCR method provides a mechanism to identify which primers in a primer pool are annealing to target gDNA. Primer utilization patterns revealed that at high annealing temperatures in the PEX PCR method, perfect match annealing predominates, while at lower annealing temperatures, primers with up to four mismatches with templates can contribute substantially to amplification. The PEX PCR method is simple to perform, is limited to PCR mixes and a single exonuclease step which can be performed without reaction cleanup, and is recommended for reactions in which degenerate primer pools are used or when mismatches between primers and template are possible.

Molybdenum Availability Is Key to Nitrate Removal in Contaminated Groundwater Environments

The concentrations of molybdenum (Mo) and 25 other metals were measured in groundwater samples from 80 wells on the Oak Ridge Reservation (ORR) (Oak Ridge, TN), many of which are contaminated with nitrate, as well as uranium and various other metals. The concentrations of nitrate and uranium were in the ranges of 0.1 μM to 230 mM and <0.2 nM to 580 μM, respectively. Almost all metals examined had significantly greater median concentrations in a subset of wells that were highly contaminated with uranium (≥126 nM). They included cadmium, manganese, and cobalt, which were 1,300- to 2,700-fold higher. A notable exception, however, was Mo, which had a lower median concentration in the uranium-contaminated wells. This is significant, because Mo is essential in the dissimilatory nitrate reduction branch of the global nitrogen cycle. It is required at the catalytic site of nitrate reductase, the enzyme that reduces nitrate to nitrite. Moreover, more than 85% of the groundwater samples contained less than 10 nM Mo, whereas concentrations of 10 to 100 nM Mo were required for efficient growth by nitrate reduction for two Pseudomonas strains isolated from ORR wells and by a model denitrifier, Pseudomonas stutzeri RCH2. Higher concentrations of Mo tended to inhibit the growth of these strains due to the accumulation of toxic concentrations of nitrite, and this effect was exacerbated at high nitrate concentrations. The relevance of these results to a Mo-based nitrate removal strategy and the potential community-driving role that Mo plays in contaminated environments are discussed.

Impact of a novel protein meal on the gastrointestinal microbiota and the host transcriptome of larval zebrafish Danio rerio

Larval zebrafish was subjected to a methodological exploration of the gastrointestinal microbiota and transcriptome. Assessed was the impact of two dietary inclusion levels of a novel protein meal (NPM) of animal origin (ragworm Nereis virens) on the gastrointestinal tract (GIT). Microbial development was assessed over the first 21 days post egg fertilization (dpf) through 16S rRNA gene-based microbial composition profiling by pyrosequencing. Differentially expressed genes in the GIT were demonstrated at 21 dpf by whole transcriptome sequencing (mRNAseq). Larval zebrafish showed rapid temporal changes in microbial colonization but domination occurred by one to three bacterial species generally belonging to Proteobacteria and Firmicutes. The high iron content of NPM may have led to an increased relative abundance of bacteria that were related to potential pathogens and bacteria with an increased iron metabolism. Functional classification of the 328 differentially expressed genes indicated that the GIT of larvae fed at higher NPM level was more active in transmembrane ion transport and protein synthesis. mRNAseq analysis did not reveal a major activation of genes involved in the immune response or indicating differences in iron uptake and homeostasis in zebrafish fed at the high inclusion level of NPM.

Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics

Despite extensive direct sequencing efforts and advanced analytical tools, reconstructing microbial genomes from soil using metagenomics have been challenging due to the tremendous diversity and relatively uniform distribution of genomes found in this system. Here we used enrichment techniques in an attempt to decrease the complexity of a soil microbiome prior to sequencing by submitting it to a range of physical and chemical stresses in 23 separate microcosms for 4 months. The metagenomic analysis of these microcosms at the end of the treatment yielded 540 Mb of assembly using standard de novo assembly techniques (a total of 559,555 genes and 29,176 functions), from which we could recover novel bacterial genomes, plasmids and phages. The recovered genomes belonged to Leifsonia (n = 2), Rhodanobacter (n = 5), Acidobacteria (n = 2), Sporolactobacillus (n = 2, novel nitrogen fixing taxon), Ktedonobacter (n = 1, second representative of the family Ktedonobacteraceae), Streptomyces (n = 3, novel polyketide synthase modules), and Burkholderia (n = 2, includes mega-plasmids conferring mercury resistance). Assembled genomes averaged to 5.9 Mb, with relative abundances ranging from rare (<0.0001%) to relatively abundant (>0.01%) in the original soil microbiome. Furthermore, we detected them in samples collected from geographically distant locations, particularly more in temperate soils compared to samples originating from high-latitude soils and deserts. To the best of our knowledge, this study is the first successful attempt to assemble multiple bacterial genomes directly from a soil sample. Our findings demonstrate that developing pertinent enrichment conditions can stimulate environmental genomic discoveries that would have been impossible to achieve with canonical approaches that focus solely upon post-sequencing data treatment.

Impaired reduction of N2O to N2 in acid soils is due to a posttranscriptional interference with the expression of nosZ

Accumulating empirical evidence over the last 60 years has shown that the reduction of N₂O to N₂ is impaired by low soil pH, suggesting that liming of acid soils may reduce N₂O emissions. This option has not gained much momentum in global change research, however, possibly due to limited understanding of why low pH interferes with N₂O reductase. We hypothesized that the reason is that denitrifying organisms in soils are unable to assemble functional N₂O reductase (N₂OR) at low pH, as shown to be the case for the model strain Paracoccus denitrificans. We tested this by experiments with bacteria extracted from soils by density gradient centrifugation. The soils were sampled from a long-term liming experiment (soil pH 4.0, 6.1, and 8.0). The cells were incubated (stirred batches, He atmosphere) at pH levels ranging from 5.7 to 7.6, while gas kinetics (NO, N₂O, and N₂) and abundances of relevant denitrification genes (nirS, nirK, and nosZ) and their transcripts were monitored. Cells from the most acidic soil (pH 4.0) were unable to reduce N₂O at any pH. These results warrant a closer inspection of denitrification communities of very acidic soils. Cells from the neutral soils were unable to produce functional N₂OR at pH values of ≤6.1, despite significant transcription of the nosZ gene. The N₂OR expressed successfully at pH 7.0, however, was functional over the entire pH range tested (5.7 to 7.6). These observations lend strong support to our hypothesis: low soil pH diminishes/prevents reduction of N₂O, primarily by precluding a successful assembly of functional N₂O reductase.

Impaired N₂O reduction in acid soils was first observed ~60 years ago, and the phenomenon has been rediscovered several times since then. The practical implication would be that the emissions of N₂O from cropped soils could be controlled by soil pH management, but this option has largely been ignored till now. One reason for this could be that the mechanisms involved have remained obscure. Here, we provide compelling evidence that the primary reason is that low pH interferes with the making of the enzyme N₂O reductase rather than the function of the enzyme if properly assembled. The implications are important for understanding how pH controls the kinetics of N₂O and N₂ production by denitrification. The improved understanding provides credibility for soil pH management as a way to mitigate N₂O emissions.

Genome sequences for three denitrifying bacterial strains isolated from a uranium- and nitrate-contaminated subsurface environment

Genome sequences for three strains of denitrifying bacteria (Alphaproteobacteria-Afipia sp. strain 1NLS2 and Hyphomicrobium denitrificans strain 1NES1; Firmicutes-Bacillus sp. strain 1NLA3E) isolated from the nitrate- and uranium-contaminated subsurface of the Oak Ridge Integrated Field Research Challenge (ORIFRC) site, Oak Ridge Reservation, TN, are reported.

Denitrifying bacterial communities affect current production and nitrous oxide accumulation in a microbial fuel cell

The biocathodic reduction of nitrate in Microbial Fuel Cells (MFCs) is an alternative to remove nitrogen in low carbon to nitrogen wastewater and relies entirely on microbial activity. In this paper the community composition of denitrifiers in the cathode of a MFC is analysed in relation to added electron acceptors (nitrate and nitrite) and organic matter in the cathode. Nitrate reducers and nitrite reducers were highly affected by the operational conditions and displayed high diversity. The number of retrieved species-level Operational Taxonomic Units (OTUs) for narG, napA, nirS and nirK genes was 11, 10, 31 and 22, respectively. In contrast, nitrous oxide reducers remained virtually unchanged at all conditions. About 90% of the retrieved nosZ sequences grouped in a single OTU with a high similarity with Oligotropha carboxidovorans nosZ gene. nirS-containing denitrifiers were dominant at all conditions and accounted for a significant amount of the total bacterial density. Current production decreased from 15.0 A·m⁻³ NCC (Net Cathodic Compartment), when nitrate was used as an electron acceptor, to 14.1 A·m⁻³ NCC in the case of nitrite. Contrarily, nitrous oxide (N₂O) accumulation in the MFC was higher when nitrite was used as the main electron acceptor and accounted for 70% of gaseous nitrogen. Relative abundance of nitrite to nitrous oxide reducers, calculated as (qnirS+qnirK)/qnosZ, correlated positively with N₂O emissions. Collectively, data indicate that bacteria catalysing the initial denitrification steps in a MFC are highly influenced by main electron acceptors and have a major influence on current production and N₂O accumulation.

Genome sequences published outside of Standards in Genomic Sciences, October - November 2012

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.

Genome sequences published outside of Standards in Genomic Sciences, July - October 2012

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.