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Heterotrophic activity, primarily driven by sulfate-reducing prokaryotes, has traditionally been linked to nitrogen fixation in the root zone of coastal marine plants, leaving the role of chemolithoautotrophy in this process unexplored. Here, we show that sulfur oxidation coupled to nitrogen fixation is a previously overlooked process providing nitrogen to coastal marine macrophytes. In this study, we recovered 239 metagenome-assembled genomes from a salt marsh dominated by the foundation plant Spartina alterniflora, including diazotrophic sulfate-reducing and sulfur-oxidizing bacteria. Abundant sulfuroxidizing bacteria encode and highly express genes for carbon fixation (RuBisCO), nitrogen fixation (nifHDK) and sulfur oxidation (oxidative-dsrAB), especially in roots stressed by sulfidic and reduced sediment conditions. Stressed roots exhibited the highest rates of nitrogen fixation and expression level of sulfur oxidation and sulfate reduction genes. Close relatives of marine symbionts from the Candidatus Thiodiazotropha genus contributed ~30% and ~20% of all sulfur-oxidizing dsrA and nitrogen-fixing nifK transcripts in stressed roots, respectively. Based on these findings, we propose that the symbiosis between S. alterniflora and sulfur-oxidizing bacteria is key to ecosystem functioning of coastal salt marshes. [ABSTRACT FROM AUTHOR]

Metagenomic Hi-C (metaHi-C) can identify contig-to-contig relationships with respect to their proximity within the same physical cell. Shotgun libraries in metaHi-C experiments can be constructed by next-generation sequencing (short-read metaHi-C) or more recent third-generation sequencing (long-read metaHi-C). However, all existing metaHi-C analysis methods are developed and benchmarked on short-read metaHi-C datasets and there exists much room for improvement in terms of more scalable and stable analyses, especially for long-read metaHi-C data. Here we report MetaCC, an efficient and integrative framework for analyzing both short-read and long-read metaHi-C datasets. MetaCC outperforms existing methods on normalization and binning. In particular, the MetaCC normalization module, named NormCC, is more than 3000 times faster than the current state-of-the-art method HiCzin on a complex wastewater dataset. When applied to one sheep gut long-read metaHi-C dataset, MetaCC binning module can retrieve 709 high-quality genomes with the largest species diversity using one single sample, including an expansion of five uncultured members from the order Erysipelotrichales, and is the only binner that can recover the genome of one important species Bacteroides vulgatus. Further plasmid analyses reveal that MetaCC binning is able to capture multi-copy plasmids. The authors develop an integrative and scalable framework to eliminate systematic biases and retrieve high-quality metagenome-assembled genomes using either long-read or short-read metagenomic Hi-C data. [ABSTRACT FROM AUTHOR]

The utilization of sustainable resources provides a path to relieving the problem of dependence on fossil resources. In this context, biomass materials have become a feasible substitute for petroleum-based materials. The development of biomass materials is booming and advanced biomass materials with various functional properties are used in many fields including medicine, electrochemistry, and environmental science. In recent years, ionic liquids have been widely used in biomass pretreatments and processing owing to their "green" characteristics and adjustable physicochemical properties. Thus, the effects of ionic liquids in biomass materials generation require further study. This review summarizes the multiple roles of ionic liquids in promoting the synthesis and application of advanced biomass materials as solvents, structural components, and modifiers. Finally, a prospective approach is proposed for producing additional higher-quality possibilities between ionic liquids and advanced biomass materials. [ABSTRACT FROM AUTHOR]

Wastewater treatment plants (WWTPs) with additional tertiary ultrafiltration membranes and ozonation treatment can improve water quality in receiving rivers. However, the impacts of WWTP upgrade (WWTP-UP) on pathogens carrying antibiotic resistance genes (ARGs) and virulence factors (VFs) in rivers remain poorly understood. In this study, ARGs, VFs, and their pathogenic hosts were investigated in three rivers impacted by large-scale WWTP-UP. A five-year sampling campaign covered the periods before and after WWTP-UP. Results showed that the abundance of total metagenome-assembled genomes (MAGs) containing both ARGs and VFs in receiving rivers did not decrease substantially after WWTP-UP, but the abundance of MAGs belonging to pathogenic genera that contain both ARGs and VFs (abbreviated as PAVs) declined markedly. Genome-resolved metagenomics further revealed that WWTP-UP not only reduced most types of VFs and ARGs in PAVs, but also effectively eliminated efflux pump and nutritional VFs carried by PAVs in receiving rivers. WWTP-UP narrowed the pathogenic host ranges of ARGs and VFs and mitigated the cooccurrence of ARGs and VFs in receiving rivers. These findings underline the importance of WWTP-UP for the alleviation of pathogens containing both ARGs and VFs in receiving rivers. [ABSTRACT FROM AUTHOR]

In the traditional extractive distillation process, organic solvents are often used as entrainers. However, environmental influence and high energy-consumption are significant problems in industrial application. In this study, a systematic screening strategy and innovative energy-saving design for ionic liquid-based extractive distillation process was proposed. The innovative energy-saving design focused on the binary minimum azeotrope mixtures isopropanol and water. Miscibility, environmental impact and physical properties (e.g., melting point and viscosity) of 30 ionic liquids were investigated. 1-Ethyl-3-methyl-imidazolium dicyanamide and 1-butyl-3-methyl-imidazolium dicyanamide were selected as candidate entrainers. Feasibility analysis of these two ionic liquids was further performed via residue curve maps, isovolatility line and temperature profiles. An innovative ionic liquid-based extractive distillation process combining distillation column and stripping column was designed and optimized with the objective function of minimizing the total annualized cost. The results demonstrate that the total annualized cost was reduced by 19.9% with 1-ethyl-3-methyl-imidazolium dicyanamide as the entrainer and by 24.3% with 1-butyl-3-methyl-imidazolium dicyanamide, compared with that of dimethyl sulfoxide. The method proposed in this study is conducive to the green and sustainable development of extractive distillation process. [ABSTRACT FROM AUTHOR]

The daily use of plastics presents a serious pollution issue due to their extremely slow degradation. Microplastics and the biofilm that grows on plastics (i.e., the plastisphere) are important subsets of plastic wastes. Many studies have been conducted to reveal the structures of the plastispheres, the driving factors for the formation of the plastisphere, and the ability of the plastispheres to degrade plastics in a variety of water bodies. However, the plastispheres related to wastewater are understudied. In this study, we used a microcosmic strategy to study the evolution of the plastispheres associated with microplastics (MPs) over time in wastewater. We found that plastic materials and water sources did not actively select and shape the plastispheres at an early stage, but the active selection for a unique niche of the plastisphere occurred after 14 d of growth. In addition, we confirmed that the alkB gene was densely present, and metagenomics showed some additional chemical reactions, which suggests that MPs are consumed by the microbes in the plastispheres. Additionally, metagenomics identified some metagenome-assembled genomes (MAGs) associated with high-density polyethylene (HDPE) and polyethylene terephthalate (PET). The identification of HDPE-associated MAGs and PET-associated MAGs further supports the notion that the selection for a unique niche of the plastisphere is driven by plastic materials and water sources (in this study, after 14 d of growth). Our discoveries bring new views on the behavior of the wastewater-associated plastisphere, especially how long it takes a wastewater plastisphere to form. [ABSTRACT FROM AUTHOR]

The hypothesis that eukaryotes originated from within the domain Archaea has been strongly supported by recent phylogenomic analyses placing Heimdallarchaeota-Wukongarchaeota branch from the Asgard superphylum as the closest known archaeal sister-group to eukaryotes. However, our understanding is still limited in terms of the relationship between eukaryotes and archaea, as well as the evolution and ecological functions of the Asgard archaea. Here, we describe three previously unknown phylum-level Asgard archaeal lineages, tentatively named Sigyn-, Freyr- and Njordarchaeota. Additional members in Wukongarchaeota and Baldrarchaeota from distinct environments are also reported here, further expanding their ecological roles and metabolic capacities. Comprehensive phylogenomic analyses further supported the origin of eukaryotes within Asgard archaea and a new lineage Njordarchaeota was supposed as the known closest branch with the eukaryotic nuclear host lineage. Metabolic reconstruction suggests that Njordarchaeota may have a heterotrophic lifestyle with capability of peptides and amino acids utilization, while Sigynarchaeota and Freyrarchaeota also have the potentials to fix inorganic carbon via the Wood-Ljungdahl pathway and degrade organic matters. Additionally, the Ack/Pta pathway for homoacetogenesis and de novo anaerobic cobalamin biosynthesis pathway were found in Freyrarchaeota and Wukongrarchaeota, respectively. Some previously unidentified eukaryotic signature proteins for intracellular membrane trafficking system, and the homologue of mu/sigma subunit of adaptor protein complex, were identified in Freyrarchaeota. This study expands the Asgard superphylum, sheds new light on the evolution of eukaryotes and improves our understanding of ecological functions of the Asgard archaea. [ABSTRACT FROM AUTHOR]

Shotgun-metagenomics may give valuable clinical information beyond the detection of potential pathogen(s). Identification of antimicrobial resistance (AMR), virulence genes and typing directly from clinical samples has been limited due to challenges arising from incomplete genome coverage. We assessed the performance of shotgun-metagenomics on positive blood culture bottles (n = 19) with periprosthetic tissue for typing and prediction of AMR and virulence profiles in Staphylococcus aureus. We used different approaches to determine if sequence data from reads provides more information than from assembled contigs. Only 0.18% of total reads was derived from human DNA. Shotgun-metagenomics results and conventional method results were consistent in detecting S. aureus in all samples. AMR and known periprosthetic joint infection virulence genes were predicted from S. aureus. Mean coverage depth, when predicting AMR genes was 209 ×. Resistance phenotypes could be explained by genes predicted in the sample in most of the cases. The choice of bioinformatic data analysis approach clearly influenced the results, i.e. read-based analysis was more accurate for pathogen identification, while contigs seemed better for AMR profiling. Our study demonstrates high genome coverage and potential for typing and prediction of AMR and virulence profiles in S. aureus from shotgun-metagenomics data. [ABSTRACT FROM AUTHOR]

The ionoSolv process is one of the most promising technologies for biomass pretreatment in a biorefinery context. In order to evaluate the transition of the ionoSolv pretreatment of biomass from bench-scale experiments to commercial scale, there is a need to get better insight in process intensification. In this work, the effects of biomass loading, particle size, pulp washing protocols and 100-fold scale up for the pretreatment of the grassy biomass Miscanthus giganteus with the IL triethylammonium hydrogen sulfate, [TEA][HSO4], are presented as a necessary step in that direction. At the bench scale, increasing biomass loading from 10 to 50 wt% reduced glucose yields from 68 to 23% due to re-precipitation of lignin onto the pulp surface. Omitting the pulp air-drying step maintained saccharification yields at 66% at 50 wt% loading due to reduced fiber hornification. 100-fold scale-up (from 10 mL to 1 L) improved the efficacy of ionoSolv pretreatment and increasing loadings from 10 to 20 wt% reduced lignin reprecipitation and led to higher glucose yields due to the improved heat and mass transfer caused by efficient slurry mixing in the reactor. Pretreatment of particle sizes of 1–3 mm was more effective than fine powders (0.18–0.85 mm) giving higher glucose yields due to reduced surface area available for lignin re-precipitation while reducing grinding energy needs. Stirred ionoSolv pretreatment showed great potential for industrialization and further process intensification after optimization of the pretreatment conditions (temperature, residence time, stirring speed), particle size and biomass loading. Pulp washing protocols need further improvement to reduce the incidence of lignin precipitation and the water requirements of lignin washing. [ABSTRACT FROM AUTHOR]

Klebsiella pneumoniae is a leading cause of antimicrobial-resistant (AMR) healthcare-associated infections, neonatal sepsis and community-acquired liver abscess, and is associated with chronic intestinal diseases. Its diversity and complex population structure pose challenges for analysis and interpretation of K. pneumoniae genome data. Here we introduce Kleborate, a tool for analysing genomes of K. pneumoniae and its associated species complex, which consolidates interrogation of key features of proven clinical importance. Kleborate provides a framework to support genomic surveillance and epidemiology in research, clinical and public health settings. To demonstrate its utility we apply Kleborate to analyse publicly available Klebsiella genomes, including clinical isolates from a pan-European study of carbapenemase-producing Klebsiella, highlighting global trends in AMR and virulence as examples of what could be achieved by applying this genomic framework within more systematic genomic surveillance efforts. We also demonstrate the application of Kleborate to detect and type K. pneumoniae from gut metagenomes. Klebsiella pneumoniae is a pathogen of increasing public health concern and antimicrobial resistance is becoming more prevalent. Here, the authors describe a K. pneumoniae genotyping tool, Kleborate, that can be used to identify lineages and detect antimicrobial resistance and virulence loci. [ABSTRACT FROM AUTHOR]

Despite recent advances in metagenomic binning, reconstruction of microbial species from metagenomics data remains challenging. Here we develop variational autoencoders for metagenomic binning (VAMB), a program that uses deep variational autoencoders to encode sequence coabundance and k-mer distribution information before clustering. We show that a variational autoencoder is able to integrate these two distinct data types without any previous knowledge of the datasets. VAMB outperforms existing state-of-the-art binners, reconstructing 29–98% and 45% more near-complete (NC) genomes on simulated and real data, respectively. Furthermore, VAMB is able to separate closely related strains up to 99.5% average nucleotide identity (ANI), and reconstructed 255 and 91 NC Bacteroides vulgatus and Bacteroides dorei sample-specific genomes as two distinct clusters from a dataset of 1,000 human gut microbiome samples. We use 2,606 NC bins from this dataset to show that species of the human gut microbiome have different geographical distribution patterns. VAMB can be run on standard hardware and is freely available at https://github.com/RasmussenLab/vamb. Metagenomics data are resolved into their constituent genomes using a new deep learning method. [ABSTRACT FROM AUTHOR]

Increasing global temperatures are predicted to stimulate soil microbial respiration. The direct and indirect impacts of warming on soil microbes, nevertheless, remain unclear. This is particularly true for understudied subsoil microbes. Here, we show that 4.5 years of whole-profile soil warming in a temperate mixed forest results in altered microbial community composition and metabolism in surface soils, partly due to carbon limitation. However, microbial communities in the subsoil responded differently to warming than in the surface. Throughout the soil profile—but to a greater extent in the subsoil—physiologic and genomic measurements show that phylogenetically different microbes could utilize complex organic compounds, dampening the effect of altered resource availability induced by warming. We find subsoil microbes had 20% lower carbon use efficiencies and 47% lower growth rates compared to surface soils, which constrain microbial communities. Collectively, our results show that unlike in surface soils, elevated microbial respiration in subsoils may continue without microbial community change in the near-term. There is much uncertainty on the response of soil microbial communities to warming, particularly in the subsoil. Here, the authors investigate microbial community and metabolism response to 4.5 years of whole-profile soil warming, finding depth-dependent effects and elevated subsoil microbial respiration. [ABSTRACT FROM AUTHOR]

Location is a crucial but often unexamined determinant of homeownership outcomes. The literature on Hispanic homeownership and the Hispanic-White homeownership gap has focused on financial, demographic, and assimilative drivers of Hispanics' tenure outcomes. However, in light of substantial changes to Hispanic settlement patterns in the 1990s and 2000s, the effects of geography on homeownership merit a closer evaluation. This article reviews the literature's current theoretical frameworks and empirical findings on the role of geography on Hispanic homeownership, and suggests avenues for further research. [ABSTRACT FROM AUTHOR]

Microorganisms play a vital role in living systems in numerous ways. In the soil or ocean environment, microbes are involved in diverse processes, such as carbon and nitrogen cycle, nutrient recycling, and energy acquisition. The relation between microbial dysbiosis and disease developments has been extensively studied. In particular, microbial communities in the human gut are associated with the pathophysiology of several chronic diseases such as inflammatory bowel disease and diabetes. Therefore, analyzing the distribution of microorganisms and their associations with the environment is a key step in understanding nature. With the advent of next-generation sequencing technology, a vast amount of metagenomic data on unculturable microbes in addition to culturable microbes has been produced. To reconstruct microbial genomes, several assembly algorithms have been developed by incorporating metagenomic features, such as uneven depth. Since it is difficult to reconstruct complete microbial genomes from metagenomic reads, contig binning approaches were suggested to collect contigs that originate from the same genome. To estimate the microbial composition in the environment, various methods have been developed to classify individual reads or contigs and profile bacterial proportions. Since microbial communities affect their hosts and environments through metabolites, metabolic profiles from metagenomic or metatranscriptomic data have been estimated. Here, we provide a comprehensive review of computational methods that can be applied to investigate microbiomes using metagenomic and metatranscriptomic sequencing data. The limitations of metagenomic studies and the key approaches to overcome such problems are discussed. [ABSTRACT FROM AUTHOR]

In previous studies of ionic liquid (IL) tolerance of numerous species of ascomycetous yeasts, two strains of Wickerhamomyces ciferrii and Galactomyces candidus had unusually high tolerance in media containing up to 5% (w/v) of the 1-ethyl-3-methylimidazolium acetate ([C2C1Im][OAc]). The study aimed at investigating whether additional strains of these species, and additional species in the Dipodascaceae family, also possess IL tolerance, and to compare sensitivity to the acetate and chloride versions of the ionic liquid. Fifty five yeast strains in the family Dipodascaceae, which encompasses genera Galactomyces, Geotrichum, and Dipodascus, and seven yeast strains of species Wickerhamomyces ciferrii were tested for ability to grow in laboratory medium containing no IL, 242 mM [C2C1Im][OAc], or 242 mM [C2C1Im]Cl, and in IL-pretreated switchgrass hydrolysate. Many yeasts exhibited tolerance of one or both ILs, with higher tolerance of the chloride anion than of the acetate anion. Different strains of the same species exhibited varying degrees of IL tolerance. Galactomyces candidus, UCDFSTs 52–260, and 50–64, had exceptionally robust growth in [C2C1Im][OAc], and also grew well in the switchgrass hydrolysate. Identification of IL tolerant and IL resistant yeast strains will facilitate studies of the mechanism of IL tolerance, which could include superior efflux, metabolism or exclusion. [ABSTRACT FROM AUTHOR]

Lignocellulose composed of complex carbohydrates and aromatic heteropolymers is one of the principal materials for the production of renewable biofuels. Lignocellulose-degrading genes from cold-adapted bacteria have a potential to increase the productivity of biological treatment of lignocellulose biomass by providing a broad range of treatment temperatures. Antarctic soil metagenomes allow to access novel genes encoding for the cold-active lignocellulose-degrading enzymes, for biotechnological and industrial applications. Here, we investigated the metagenome targeting cold-adapted microbes in Antarctic organic matter-rich soil (KS 2-1) to mine lignolytic and celluloytic enzymes by performing single molecule, real-time metagenomic (SMRT) sequencing. In the assembled Antarctic metagenomic contigs with relative long reads, we found that 162 (1.42%) of total 11,436 genes were annotated as carbohydrate-active enzymes (CAZy). Actinobacteria, the dominant phylum in this soil's metagenome, possessed most of candidates of lignocellulose catabolic genes like glycoside hydrolase families (GH13, GH26, and GH5) and auxiliary activity families (AA7 and AA3). The predicted lignocellulose degradation pathways in Antarctic soil metagenome showed synergistic role of various CAZyme harboring bacterial genera including Streptomyces, Streptosporangium, and Amycolatopsis. From phylogenetic relationships with cellular and environmental enzymes, several genes having potential for participating in overall lignocellulose degradation were also found. The results indicated the presence of lignocellulose-degrading bacteria in Antarctic tundra soil and the potential benefits of the lignocelluolytic enzymes as candidates for cold-active enzymes which will be used for the future biofuel-production industry. [ABSTRACT FROM AUTHOR]

It is unclear how autonomy-related parenting processes are associated with Latinx adolescent adjustment. This study uses Latent Profile Analysis to identify typologies of parental monitoring and parent–adolescent conflict and examines their association with Latinx youth's school performance and depressive symptoms. The sample included 248 Latinx 9th and 10th graders (50% female) who completed surveys during fall (Time 1) and spring (Time 2) semesters of the school year. When compared to a high monitoring/low conflict parenting profile, a moderate monitoring/moderate conflict profile was associated with stronger declines in school performance; for boys, a high monitoring/moderately high conflict profile also was associated with greater increases in depressive symptoms. For Latinx immigrant families, researchers should consider monitoring and conflict as co-occurring processes. [ABSTRACT FROM AUTHOR]

Although shotgun metagenomic sequencing of microbiome samples enables partial reconstruction of strain-level community structure, obtaining high-quality microbial genome drafts without isolation and culture remains difficult. Here, we present an application of read clouds, short-read sequences tagged with long-range information, to microbiome samples. We present Athena, a de novo assembler that uses read clouds to improve metagenomic assemblies. We applied this approach to sequence stool samples from two healthy individuals and compared it with existing short-read and synthetic long-read metagenomic sequencing techniques. Read-cloud metagenomic sequencing and Athena assembly produced the most comprehensive individual genome drafts with high contiguity (>200-kb N50, fewer than ten contigs), even for bacteria with relatively low (20×) raw short-read-sequence coverage. We also sequenced a complex marine-sediment sample and generated 24 intermediate-quality genome drafts (>70% complete, <10% contaminated), nine of which were complete (>90% complete, <5% contaminated). Our approach allows for culture-free generation of high-quality microbial genome drafts by using a single shotgun experiment. [ABSTRACT FROM AUTHOR]

Determining the phylogenetic origin of mitochondria is key to understanding the ancestral mitochondrial symbiosis and its role in eukaryogenesis. However, the precise evolutionary relationship between mitochondria and their closest bacterial relatives remains hotly debated. The reasons include pervasive phylogenetic artefacts as well as limited protein and taxon sampling. Here we developed a new model of protein evolution that accommodates both across-site and across-branch compositional heterogeneity. We applied this site-and-branch-heterogeneous model (MAM60 + GFmix) to a considerably expanded dataset that comprises 108 mitochondrial proteins of alphaproteobacterial origin, and novel metagenome-assembled genomes from microbial mats, microbialites and sediments. The MAM60 + GFmix model fits the data much better and agrees with analyses of compositionally homogenized datasets with conventional site-heterogenous models. The consilience of evidence thus suggests that mitochondria are sister to the Alphaproteobacteria to the exclusion of MarineProteo1 and Magnetococcia. We also show that the ancestral presence of the crista-developing mitochondrial contact site and cristae organizing system (a mitofilin-domain-containing Mic60 protein) in mitochondria and the Alphaproteobacteria only supports their close relationship., (© 2022. The Author(s), under exclusive licence to Springer Nature Limited.)

Preterm infants exhibit different microbiome colonization patterns relative to full-term infants, and it is speculated that the hospital room environment may contribute to infant microbiome development. Here, we present a genome-resolved metagenomic study of microbial genotypes from the gastrointestinal tracts of infants and from the neonatal intensive care unit (NICU) room environment. Some strains detected in hospitalized infants also occur in sinks and on surfaces, and belong to species such as Staphylococcus epidermidis, Enterococcus faecalis, Pseudomonas aeruginosa, and Klebsiella pneumoniae, which are frequently implicated in nosocomial infection and preterm infant gut colonization. Of the 15 K. pneumoniae strains detected in the study, four were detected in both infant gut and room samples. Time series experiments showed that nearly all strains associated with infant gut colonization can be detected in the room after, and often before, detection in the gut. Thus, we conclude that a component of premature infant gut colonization is the cycle of microbial exchange between the room and the occupant. [ABSTRACT FROM AUTHOR]

Community receptivity, a critical component in integration processes, is a place's collective response to newcomers. It is a constructed context in which the experiences of settlement and adjustment for both immigrants and non-immigrants occur. Receptivity is fluid, shaped by multi-scalar components of a community's political, economic, social, and cultural spheres. In traditional gateways, the evolving interplay of long-established forces guides receptivity. But in new gateways, front line providers that encounter the initial settlement needs of immigrants are the vanguard of constructing the broader community's warmth of immigrant welcome. This case study of three elementary schools in Charlotte, NC demonstrates the role of public schools as a site of receptivity's early construction within an emerging gateway. We argue that teachers are creating receptivity building blocks within their classrooms, guiding the construction of receptivity within their schools, among the school board, the school district, and the city as a whole. [ABSTRACT FROM AUTHOR]

We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity. [ABSTRACT FROM AUTHOR]

Part 2 of the review discusses modern processes for biotechnological conversion of lignocellulosic biomass into the valuable chemicals. It also recognizes the new approaches toward the development of more efficient enzymes for the depolymerization of biomass and the properties of the microorganisms employed in the fermentation of the biomass-derived sugars. Various biotechnological approaches to the fermentation of the depolymerized biomass products are described, including SHF, SSF, NSSF, SSFF, SSCF, and CBP. It is demonstrated that that the main tendencies for development of the new technologies for biotechnological biomass processing are the application of genetic engineering, synthetic biology and reduction of the number of processing steps. Application of one-pot processing of lignocellulosic biomass is promising for development of the new and efficient manufacturing technologies for production of valuable chemicals. [ABSTRACT FROM AUTHOR]

Among the many types of lignocellulosic biomass pretreatment methods, the use of ionic liquids (ILs) is regarded as one of the most promising strategies. In this study, the effects of four kinds of ILs for pretreatment of lignocellulosic biomass such as bagasse, eucalyptus, and cedar were evaluated. In direct ethanol fermentation from biomass incorporated with ILs by cellulase-displaying yeast, 1-butyl-3-methylimidazolium acetate ([Bmim][OAc]) was the most effective IL. The ethanol production and yield from [Bmim][OAc]-pretreated bagasse reached 0.81 g/L and 73.4% of the theoretical yield after fermentation for 96 h. The results prove the initial concept, in which the direct fermentation from lignocellulosic biomass effectively promoted by the pretreatment with IL. [ABSTRACT FROM AUTHOR]

Ionic liquid (IL) based pretreatment of lignocellulosic biomass for facilitating efficient enzymatic saccharification has emerged as an environmentally benign approach that offers several advantages over conventional strategies. However, residues of ionic liquid left in the pretreated biomass may cause inactivation of saccharifying enzymes thus, necessitating the requirement of ionic liquid-stable enzymes. Cost-effective production of industrial enzymes is always desired to enhance the overall process economy. Current study reports IL-stable cellulase production from a newly isolated bacterium Bacillus subtilis G. Design of experiment (DoE) based on response surface methodology was used in sequential manner for optimizing cultural and environmental variables to enhance cellulase production by 2.66-fold. IL-stable cellulase was used for saccharification of IL-pretreated pine needle biomass (PNB) with 1-ethyl-3-methylimidazolium methanesulfonate in a consolidated single pot process i.e. one pot consolidated bioprocess (OPCB). The saccharification efficiency of 23.57 % was observed under OPCB. The hydrolsate obtained was fermented by dual culture of yeast i.e. Saccharomyces cereviasie NCIM 3078 and Pichia stipitis NCIM 3497, and a yield of 0.092 g ethanol/g of PNB was obtained with fermentation efficiency of 25.62 %. This study is first ever where-in IL-stable cellulase production is accomplished using agroindustrial residues by employing DoE, and assessed for its application potential under OPCB for saccharification of IL-pretreated PNB. IL-stable cellulases would not only preclude expensive washing step following IL-pretreatment of biomass, but their application in a consolidated single pot process (OPCB) offers numerous technoeconomic advantages over conventional multi pot processes. Graphical Abstract: Production of ionic liquid (IL) tolerant cellulase from Bacillus subtilis G was enhanced by 2.66-fold using response surface methodology. Cellulase was assessed for its saccharification potential on IL-pretreated pine needle biomass under one pot consolidated bioprocess, and the hydrolysate was fermented to ethanol using Saccharomyces cereviasie and Pichia stipitis. [ABSTRACT FROM AUTHOR]

Culture-independent microbiome studies have increased our understanding of the complexity and metabolic potential of microbial communities. However, to understand the contribution of individual microbiome members to community functions, it is important to determine which bacteria are actively replicating. We developed an algorithm, iRep, that uses draft-quality genome sequences and single time-point metagenome sequencing to infer microbial population replication rates. The algorithm calculates an index of replication (iRep) based on the sequencing coverage trend that results from bi-directional genome replication from a single origin of replication. We apply this method to show that microbial replication rates increase after antibiotic administration in human infants. We also show that uncultivated, groundwater-associated, Candidate Phyla Radiation bacteria only rarely replicate quickly in subsurface communities undergoing substantial changes in geochemistry. Our method can be applied to any genome-resolved microbiome study to track organism responses to varying conditions, identify actively growing populations and measure replication rates for use in modeling studies. [ABSTRACT FROM AUTHOR]

In this study, the effect of the thermophilic fungi of composts was analysed on the fungal composition of the air above. Air samples were collected with an Andersen air sampler at 1.5 m height in three large industrial composting facilities treating different waste types. Repetition was collected on three calm and rain-free days of three consecutive weeks in October 2011, in January, April and July 2012; five plates were exposed successively per sampling day. Compost samples were also collected (averaging 1 kg/compost piles). Air and compost samples were cultured at 50 °C. The thermophilic fungal composition of the air near the compost piles of different waste types differed significantly ( p < 0.05) from that of the control site above a grassland ecosystem at each sampling time. Seasonal differences could be detected regarding the total number of thermophilic fungi in the air near the agricultural and horticultural compost types, but smaller differences were found near the municipal compost type. A total of 13 and 11 fungal species were detected in the compost and air samples where the dominant species were Thermomyces lanuginosus and Rasamsonia emersonii, respectively. The concentration of airborne thermophilic fungi was higher near the horticultural compost type and lower near the municipal compost. The results suggest that the differences between the incidences of some species in composts and associated aerosols refer to spore ontogeny and biological mechanisms of spore liberation. [ABSTRACT FROM AUTHOR]

Literature published mainly between 1995 and 2015 in the field of investigations aimed at finding promising new catalysts for the industrial processing of polysaccharide components of lignocellulose biomass, for new methods to achieve these processes, and for new ways of transforming polysaccharides into valuable chemicals and fuel is reviewed. In the first section, modern methods for activating lignocellulose biomass in order to separate main components and/or treat polysaccharide feedstock (cellulose, hemicelluloses) for further processing are considered. The second will deal with catalytic acidic transformations of these components into monosaccharides and furans. The third will focus on with the main focus on the production of 5-hydroxymethylfurfurol the application of biotechnological enzymatic methods for producing valuable chemicals such as ethanol, isobutanol, lactic acid. [ABSTRACT FROM AUTHOR]

The structure, composition, and developmental patterns of multi-species biofilms are analyzed, as are the mechanisms of interaction of their microbial components. The main methodological approaches used for analysis of multi-species biofilms, including omics technologies, are characterized. Environmental communities (cyanobacterial mats and methanotrophic communities), as well as typical multi-species communities of medical importance (oral cavity, skin, and intestinal microbiomes), are described. A special section deals with the role of multi-species biofilms in such biotechnological processes as wastewater treatment, heavy metal removal, corrosion control, and environmental bioremediation. [ABSTRACT FROM AUTHOR]

Downward fluxes of particulate organic matter (POM) are the major process for sequestering atmospheric CO2 into aquatic sediments for thousands of years. Budget calculations of the biological carbon pump are heavily based on the ratio between carbon export (sedimentation) and remineralization (release to the atmosphere). Current methodologies determine microbial dynamics on POM using closed vessels, which are strongly biased towards heterotrophy due to rapidly changing water chemistry (Bottle Effect). We developed a flow-through rolling tank for long term studies that continuously maintains POM at near in-situ conditions. There, bacterial communities resembled in-situ communities and greatly differed from those in the closed systems. The active particle-associated community in the flow-through system was stable for days, contrary to hours previously reported for closed incubations. In contrast to enhanced respiration rates, the decrease in photosynthetic rates on particles throughout the incubation was much slower in our system than in traditional ones. These results call for reevaluating experimentally-derived carbon fluxes estimated using traditional methods. [ABSTRACT FROM AUTHOR]

Microorganisms do not exist in isolation in the environment. Instead, they form complex communities among themselves as well as with their hosts. Different forms of interactions not only shape the composition of these communities but also define how these communities are established and maintained. The kinds of interaction a bacterium can employ are largely encoded in its genome. This allows us to deploy a genomescale modeling approach to understand, and ultimately predict, the complex and intertwined relationships in which microorganisms engage. So far, most studies on microbial communities have been focused on synthetic co-cultures and simple communities. However, recent advances in molecular and computational biology now enable bottom up methods to be deployed for complex microbial communities from the environment to provide insight into the intricate and dynamic interactions in which microorganisms are engaged. These methods will be applicable for a wide range of microbial communities involved in industrial processes, as well as understanding, preserving and reconditioning natural microbial communities present in soil, water, and the human microbiome. [ABSTRACT FROM AUTHOR]

Ethnic enterprises are growing rapidly in urban areas across the United States. Anecdotal evidence from around the country reports many success stories of how ethnic businesses transform communities; however, researchers have not provided a systematic review of the role of ethnic businesses in community developing. In practice, ethnic businesses have not been formally incorporated in local planning and development process. This article provides a systematic review of the multi-faceted ways ethnic businesses contribute to community building and neighborhood development. In addition to surveying the current literature, we also chose three communities for a focused review: Buford Highway in Atlanta, Monterey Park in Los Angeles, and Sunset Park in New York. A framework is developed to evaluate the economic, physical, social/cultural, and political effects that ethnic businesses exert on communities. We find that ethnic businesses can serve local economic interests and community-level cohesion and accrue economic, social, physical, and political benefits to their respective communities. These include serving the unmet market needs of certain neighborhoods and households, creating job opportunities and generating revenues, revitalizing and fueling the commercial development of abandoned communities, organizing and promoting social life and cultural diversity, as well as contributing their collective interest and voice in local communities. We argue that ethnic businesses should be better incorporated into urban policies in community economic development. [ABSTRACT FROM AUTHOR]

The review presents recent data on mechanisms for the microbial transformation of trace elements in natural bioabiotic systems (soils, sediments, sludge, and aquatic systems). Processes of oxidation, reduction, and biomethylation of trace elements by microorganisms are described in detail. Toxic effects of microbiologically transformed compounds on the environment are also shown. [ABSTRACT FROM AUTHOR]

A model for metabolism of the last bacterial common ancestor based on biomimetic analysis of the metabolic systems of phylogenetically ancient bacteria is developed. The mechanism of natural selection and evolution of the autocatalytic chemical systems under the effect of natural homeostatic parameters, such as chemical potentials, temperature, and pressure of environment is proposed. Competition between particular parts of the autocatalytic network with positive-plus-negative feedback resulted in the formation of particular systems of primary autotrophic, mixotrophic, and heterotrophic metabolism. The model of the last common ancestor as a combination of coupled metabolic cycles among population of protocells is discussed. Physicochemical features of these metabolic cycles determined the major principles of natural selection towards ancestral bacterial taxa. [ABSTRACT FROM AUTHOR]

This study examines and compares how the spatial arrangements of Spanish speakers have changed over time in a traditional immigrant gateway, Chicago, and in an emerging immigrant gateway, Atlanta. Using the 1990 and 2000 U.S. Census data, spatial autocorrelation analysis confirms that Spanish-language neighborhoods continue to be in the city and the suburbs of Chicago. Atlanta’s Spanish-language neighborhoods, on the other hand, are mainly located in the suburbs where major growth took place over the decade. However, Spanish-language neighborhoods in both the city and suburbs of Atlanta and Chicago share similar characteristics: higher percentages of residents who are foreign-born and limited English proficient, and households with low levels of income. While the model of spatial assimilation is still relevant to our understanding of residential patterns among contemporary immigrants and their descendants, the interpretation of findings, including those for new destinations such as Atlanta where large-scale immigration occurred after suburbanization, should place less emphasis on the central city/suburb distinction and suburban homogeneity. The growing diversity in language use among residents necessitates the provision of accessible social services and information. [ABSTRACT FROM AUTHOR]

Reactions involving H2, N2, CO, CO2 and CH4 are likely to have been central to the origin of life. This is indicated by the active-site structures of the enzymes involved, which are often reminiscent of minerals. Through the combined efforts of protein crystallography, various types of spectroscopy, theoretical calculations and model chemistry, it has been possible to put forward plausible mechanisms for gas-based metabolism by extant microorganisms. Although the reactions are based on metal centres, the protein matrix regulates reactivity and substrate and product trafficking through internal pathways, specific ligation and dielectricity. [ABSTRACT FROM AUTHOR]

We know very little about the metabolic functioning and evolutionary dynamics of microbial communities. Recent advances in comprehensive, sequencing-based methods, however, are laying a molecular foundation for new insights into how microbial communities shape the Earth's biosphere. Here we explore the convergence of microbial ecology, genomics, biological mass spectrometry and informatics that form the new field of microbial community proteogenomics. We discuss the first applications of proteogenomics and its potential for studying the physiology, ecology and evolution of microbial populations and communities. [ABSTRACT FROM AUTHOR]

This essay places the early modern origins of the ethico-legal structure of medicine, in which eventually by exclusion or inclusion, dental activity shared, in the Humanist environment of the Italian Renaissance as it was imported into England in the first years of the sixteenth century. There were two linked stages to this, the first supported by the genius of Thomas Linacre (1460-1524), and the second by the administrative ability of Sir Thomas More (1478-1535). This paper concentrates on the evidence for the intellectual basis of More's medical legislation, and that which was made shortly after his death. [ABSTRACT FROM AUTHOR]

Phototrophic microbial mats dominated terrestrial ecosystems for billions of years, largely causing, through cyanobacterial oxygenic photosynthesis, but also undergoing, the Great Oxidation Event approximately 2.5 billion years ago. Taking a space-for-time approach based on the universality of core metabolic pathways expressed at ecosystem level, we studied gene content and co-occurrence networks in high-diversity metagenomes from spatially close microbial mats along a steep redox gradient. The observed functional shifts suggest that anoxygenic photosynthesis was present but not predominant under early Precambrian conditions, being accompanied by other autotrophic processes. Our data also suggest that, in contrast to general assumptions, anoxygenic photosynthesis largely expanded in parallel with the subsequent evolution of oxygenic photosynthesis and aerobic respiration. Finally, our observations might represent space-for-time evidence that the Wood-Ljungdahl carbon fixation pathway dominated phototrophic mats in early ecosystems, whereas the Calvin cycle probably evolved from pre-existing variants before becoming the dominant contemporary form of carbon fixation.

A female infant presented with signs of general muscle hypotonia and increasing hypertrophy of the heart muscle. There was a constant lactic acidosis worsened after glucose intake. Serum lactate levels were increased up to 6.7 mmol/l. Serum alanine levels reached maximum concentrations of 2,800 mumol/l. The patient died after sudden cardiac arrest at 22 months of age. Histology of the heart showed the pattern of foamy myocardial transformation with accumulation of mitochondria and an increased glycogen content. Biochemical analysis of the skeletal muscle and the heart demonstrated signs of a disturbed respiratory chain. The content of cytochrome aa3 protein was decreased in skeletal muscle and heart mitochondria. It is suggested that respiratory chain defects may be the cause of foamy myocardial transformation of the heart. [ABSTRACT FROM AUTHOR]

Deposit-feeding invertebrates are proposed bioremediators in microbial-driven sediment-based aquaculture effluent treatment systems. We elucidate the role of the sediment reduction-oxidation (redox) regime in structuring benthic bacterial communities, having direct implications for bioremediation potential and deposit-feeder nutrition. The sea cucumber Holothuria scabra was cultured on sediments under contrasting redox regimes; fully oxygenated (oxic) and redox stratified (oxic-anoxic). Taxonomically, metabolically and functionally distinct bacterial communities developed between the redox treatments with the oxic treatment supporting the greater diversity; redox regime and dissolved oxygen levels were the main environmental drivers. Oxic sediments were colonised by nitrifying bacteria with the potential to remediate nitrogenous wastes. Percolation of oxygenated water prevented the proliferation of anaerobic sulphate-reducing bacteria, which were prevalent in the oxic-anoxic sediments. At the predictive functional level, bacteria within the oxic treatment were enriched with genes associated with xenobiotics metabolism. Oxic sediments showed the greater bioremediation potential; however, the oxic-anoxic sediments supported a greater sea cucumber biomass. Overall, the results indicate that bacterial communities present in fully oxic sediments may enhance the metabolic capacity and bioremediation potential of deposit-feeder microbial systems. This study highlights the benefits of incorporating deposit-feeding invertebrates into effluent treatment systems, particularly when the sediment is oxygenated. [ABSTRACT FROM AUTHOR]