Microbial Extraction of Cobalt and Nickel from Lateritic Chromite Overburden using Aspergillus wentii

ABSTRACT Low-grade nickeliferous lateritic ore from Sukinda region of Orissa, India, was subjected to biohydrometallurgical treatment for the extraction of nickel and cobalt. The mineralogical studies reveal that nickel is entrapped in goethite matrix while cobalt is associated with the manganese phase. Aspergillus wentii NCIM 667, a citric acid producing fungal strain, was used for direct (one step and two step) and indirect (using culture filtrate) leaching of the metals under different conditions. The effect of varying pulp density (2%, 5%, 8%) and culture medium composition (viz. molasses and sucrose media) was investigated and the leaching conditions optimized. It was found that a maximum of 49.29% Ni and 35.18% Co could be recovered from the heat-treated lateritic chromite overburden by the culture filtrate bioleaching at 80°C with 2% pulp density

Metatranscriptomic Sequencing of a Cyanobacterial Soil-Surface Consortium with and without a Diverse Underlying Soil Microbiome.

Soil surface consortia are easily observed and sampled, allowing examination of their interactions with soil microbiomes. Here, we present metatranscriptomic sequences from Dark Green 1 (DG1), a cyanobacterium-based soil surface consortium, in the presence and absence of an underlying soil microbiome and/or urea

High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1T (DSM 17521T) isolated from muddy waters of a drainage system in Chandigarh, India

Pontibacter roseus Suresh et al 2006 is a member of genus Pontibacter family Cytophagaceae, class Cytophagia. While the type species of the genus Pontibacter actiniarum was isolated in 2005 from a marine environment, subsequent species of the same genus have been found in different types of habitats ranging from seawater, sediment, desert soil, rhizosphere, contaminated sites, solar saltern andmuddy water. Here we describe the features of Pontibacter roseus strain SRC-1T along with its complete genome sequence and annotation from a culture of DSM 17521T. The 4,581,480 bp long draft genome consists of 12 scaffolds with 4,003 protein-coding and 50 RNA genes and is a part of Genomic encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project

Genome sequence of <i>Oceanicola</i> sp. strain MCTG156(1a) isolated from a Scottish coastal phytoplankton net sample

ABSTRACT Oceanicola sp. strain MCTG156(1a) was isolated from a phytoplankton net sample collected on the west coast of Scotland and selected based on its ability to degrade polycyclic aromatic hydrocarbons. Here, we present the genome sequence of this strain, which comprises 3,881,122 bp with 3,949 genes and an average G+C content of 62.7%. </jats:p

Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels

International audienceClostridium phytofermentans was isolated from forest soil and is distinguished by its capacity to directly ferment plant cell wall polysaccharides into ethanol as the primary product, suggesting that it possesses unusual catabolic pathways. The objective of the present study was to understand the molecular mechanisms of biomass conversion to ethanol in a single organism, Clostridium phytofermentans, by analyzing its complete genome and transcriptome during growth on plant carbohydrates. The saccharolytic versatility of C. phytofermentans is reflected in a diversity of genes encoding ATP-binding cassette sugar transporters and glycoside hydrolases, many of which may have been acquired through horizontal gene transfer. These genes are frequently organized as operons that may be controlled individually by the many transcriptional regulators identified in the genome. Preferential ethanol production may be due to high levels of expression of multiple ethanol dehydrogenases and additional pathways maximizing ethanol yield. The genome also encodes three different proteinaceous bacterial microcompartments with the capacity to compartmentalize pathways that divert fermentation intermediates to various products. These characteristics make C. phytofermentans an attractive resource for improving the efficiency and speed of biomass conversion to biofuels

Collating and validating indigenous and local knowledge to apply multiple knowledge systems to an environmental challenge: A case-study of pollinators in India

There is an important role for indigenous and local knowledge in a Multiple Evidence Base to make decisions about the use of biodiversity and its management. This is important both to ensure that the knowledge base is complete (comprising both scientific and local knowledge) and to facilitate participation in the decision making process. We present a novel method to gather evidence in which we used a peer-to-peer validation process among farmers that we suggest is analogous to scientific peer review. We used a case-study approach to trial the process focussing on pollinator decline in India. Pollinator decline is a critical challenge for which there is a growing evidence base, however, this is not the case world–wide. In the state of Orissa, India, there are no validated scientific studies that record historical pollinator abundance, therefore local knowledge can contribute substantially and may indeed be the principle component of the available knowledge base. Our aim was to collate and validate local knowledge in preparation for integration with scientific knowledge from other regions, for the purpose of producing a Multiple Evidence Base to develop conservation strategies for pollinators. Farmers reported that vegetable crop yields were declining in many areas of Orissa and that the abundance of important insect crop pollinators has declined sharply across the study area in the last 10–25 years, particularly Apis cerana, Amegilla sp. and Xylocopa sp. Key pollinators for commonly grown crops were identified; both Apris cerana and Xylocopa sp. were ranked highly as pollinators by farmer participants. Crop yield declines were attributed to soil quality, water management, pests, climate change, overuse of chemical inputs and lack of agronomic expertise. Pollinator declines were attributed to the quantity and number of pesticides used. Farmers suggested that fewer pesticides, more natural habitat and the introduction of hives would support pollinator populations. This process of knowledge creation was supported by participants, which led to this paper being co-authored by both scientists and farmers

Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot

The rocky, seasonally-dry and nutrient-impoverished soils of the Brazilian campos rupestres impose severe growth-limiting conditions on plants. Species of a dominant plant family, Velloziaceae, are highly specialized to low-nutrient conditions and seasonal water availability of this environment, where phosphorus (P) is the key limiting nutrient. Despite plant-microbe associations playing critical roles in stressful ecosystems, the contribution of these interactions in the campos rupestres remains poorly studied. Here we present the first microbiome data of Velloziaceae spp. thriving in contrasting substrates of campos rupestres. We assessed the microbiomes of Vellozia epidendroides, which occupies shallow patches of soil, and Barbacenia macrantha, growing on exposed rocks. The prokaryotic and fungal profiles were assessed by rRNA barcode sequencing of epiphytic and endophytic compartments of roots, stems, leaves and surrounding soil/rocks. We also generated root and substrate (rock/soil)-associated metagenomes of each plant species. We foresee that these data will contribute to decipher how the microbiome contributes to plant functioning in the campos rupestres, and to unravel new strategies for improved crop productivity in stressful environments6COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIOR - CAPESFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESP88881.068071/2014-012016/23218-0Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) [2016/23218-0]; U.S. Department of Energy Joint Genome Institute (DOE-JGI)United States Department of Energy (DOE) [CSP 503222]; Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES)CAPES [88881.068071/2014-01]; FAPESPFundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) [2018/04240-0]; CAPESCAPES; Office of Science of the U.S. Department of EnergyUnited States Department of Energy (DOE) [DE-AC02-05CH11231

Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota

The North Temperate Lakes Long-Term Ecological Research (NTL-LTER) program has been extensively used to improve understanding of how aquatic ecosystems respond to environmental stressors, climate fluctuations, and human activities. Here, we report on the metagenomes of samples collected between 2000 and 2019 from Lake Mendota, a freshwater eutrophic lake within the NTL-LTER site. We utilized the distributed metagenome assembler MetaHipMer to coassemble over 10 terabases (Tbp) of data from 471 individual Illumina-sequenced metagenomes. A total of 95,523,664 contigs were assembled and binned to generate 1,894 non-redundant metagenome-assembled genomes (MAGs) with ≥50% completeness and ≤10% contamination. Phylogenomic analysis revealed that the MAGs were nearly exclusively bacterial, dominated by Pseudomonadota (Proteobacteria, N = 623) and Bacteroidota (N = 321). Nine eukaryotic MAGs were identified by eukCC with six assigned to the phylum Chlorophyta. Additionally, 6,350 high-quality viral sequences were identified by geNomad with the majority classified in the phylum Uroviricota. This expansive coassembled metagenomic dataset provides an unprecedented foundation to advance understanding of microbial communities in freshwater ecosystems and explore temporal ecosystem dynamics

The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole

Eukaryotic phytoplankton are responsible for at least 20% of annual global carbon fixation. Their diversity and activity are shaped by interactions with prokaryotes as part of complex microbiomes. Although differences in their local species diversity have been estimated, we still have a limited understanding of environmental conditions responsible for compositional differences between local species communities on a large scale from pole to pole. Here, we show, based on pole-to-pole phytoplankton metatranscriptomes and microbial rDNA sequencing, that environmental differences between polar and non-polar upper oceans most strongly impact the large-scale spatial pattern of biodiversity and gene activity in algal microbiomes. The geographic differentiation of co-occurring microbes in algal microbiomes can be well explained by the latitudinal temperature gradient and associated break points in their beta diversity, with an average breakpoint at 14 °C ± 4.3, separating cold and warm upper oceans. As global warming impacts upper ocean temperatures, we project that break points of beta diversity move markedly pole-wards. Hence, abrupt regime shifts in algal microbiomes could be caused by anthropogenic climate change

Multiomics in the central Arctic Ocean for benchmarking biodiversity change

Multiomics approaches need to be applied in the central Arctic Ocean to benchmark biodiversity change and to identify novel species and their genes. As part of MOSAiC, EcoOmics will therefore be essential for conservation and sustainable bioprospecting in one of the least explored ecosystems on Earth