Assembling large, complex environmental metagenomes

The large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires significant computational resources. We apply two pre-assembly filtering approaches, digital normalization and partitioning, to make large metagenome assemblies more comput\ ationaly tractable. Using a human gut mock community dataset, we demonstrate that these methods result in assemblies nearly identical to assemblies from unprocessed data. We then assemble two large soil metagenomes from matched Iowa corn and native prairie soils. The predicted functional content and phylogenetic origin of the assembled contigs indicate significant taxonomic differences despite similar function. The assembly strategies presented are generic and can be extended to any metagenome; full source code is freely available under a BSD license.Comment: Includes supporting informatio

Use of Remote-Sensing Imagery to Estimate Corn Grain Yield

Remote sensing—the process of acquiring information about objects from remote platforms such as ground-based booms, aircraft, or satellites—is a potentially important source of data for site-specific crop management, providing both spatial and temporal information. Our objective was to use remotely sensed imagery to compare different vegetation indices as a means of assessing canopy variation and its resultant impact on corn (Zea mays L.) grain yield. Treatments consisted of five N rates and four hybrids, which were grown under irrigation near Shelton, NE on a Hord silt loam in 1997 and 1998. Imagery data with 0.5-m spatial resolution were collected from aircraft on several dates during both seasons using a multispectral, four-band [blue, green, red, and near-infrared reflectance] digital camera system. Imagery was imported into a geographical information system (GIS) and then geo-registered, converted into reflectance, and used to compute three vegetation indices. Grain yield for each plot was determined at maturity. Results showed that green normalized difference vegetation index (GNDVI) values derived from images acquired during midgrain filling were the most highly correlated with grain yield; maximum correlations were 0.7 and 0.92 in 1997 and 1998, respectively. Normalizing GNDVI and grain yield variability within hybrids improved the correlations in both years, but more dramatic increases were observed in 1997 (0.7 to 0.82) than in 1998 (0.92 to 0.95). This suggested GNDVI acquired during midgrain filling could be used to produce relative yield maps depicting spatial variability in fields, offering a potentially attractive alternative to use of a combine yield monitor

New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes

Deforestation in the Brazilian Amazon occurs at an alarming rate, which has broad effects on global greenhouse gas emissions, carbon storage, and biogeochemical cycles. In this study, soil metagenomes and metagenome-assembled genomes (MAGs) were analyzed for alterations to microbial community composition, functional groups, and putative physiology as it related to land-use change and tropical soil. A total of 28 MAGs were assembled encompassing 10 phyla, including both dominant and rare biosphere lineages. Amazon Acidobacteria subdivision 3, Melainabacteria, Microgenomates, and Parcubacteria were found exclusively in pasture soil samples, while Candidatus Rokubacteria was predominant in the adjacent rainforest soil. These shifts in relative abundance between land-use types were supported by the different putative physiologies and life strategies employed by the taxa. This research provides unique biological insights into candidate phyla in tropical soil and how deforestation may impact the carbon cycle and affect climate change

The Airborne Metagenome in an Indoor Urban Environment

The indoor atmosphere is an ecological unit that impacts on public health. To investigate the composition of organisms in this space, we applied culture-independent approaches to microbes harvested from the air of two densely populated urban buildings, from which we analyzed 80 megabases genomic DNA sequence and 6000 16S rDNA clones. The air microbiota is primarily bacteria, including potential opportunistic pathogens commonly isolated from human-inhabited environments such as hospitals, but none of the data contain matches to virulent pathogens or bioterror agents. Comparison of air samples with each other and nearby environments suggested that the indoor air microbes are not random transients from surrounding outdoor environments, but rather originate from indoor niches. Sequence annotation by gene function revealed specific adaptive capabilities enriched in the air environment, including genes potentially involved in resistance to desiccation and oxidative damage. This baseline index of air microbiota will be valuable for improving designs of surveillance for natural or man-made release of virulent pathogens

Substrate Type Determines Metagenomic Profiles from Diverse Chemical Habitats

Environmental parameters drive phenotypic and genotypic frequency variations in microbial communities and thus control the extent and structure of microbial diversity. We tested the extent to which microbial community composition changes are controlled by shifting physiochemical properties within a hypersaline lagoon. We sequenced four sediment metagenomes from the Coorong, South Australia from samples which varied in salinity by 99 Practical Salinity Units (PSU), an order of magnitude in ammonia concentration and two orders of magnitude in microbial abundance. Despite the marked divergence in environmental parameters observed between samples, hierarchical clustering of taxonomic and metabolic profiles of these metagenomes showed striking similarity between the samples (>89%). Comparison of these profiles to those derived from a wide variety of publically available datasets demonstrated that the Coorong sediment metagenomes were similar to other sediment, soil, biofilm and microbial mat samples regardless of salinity (>85% similarity). Overall, clustering of solid substrate and water metagenomes into discrete similarity groups based on functional potential indicated that the dichotomy between water and solid matrices is a fundamental determinant of community microbial metabolism that is not masked by salinity, nutrient concentration or microbial abundance

Use of Remote-Sensing Imagery to Estimate Corn Grain Yield

Remote sensing—the process of acquiring information about objects from remote platforms such as ground-based booms, aircraft, or satellites—is a potentially important source of data for site-specific crop management, providing both spatial and temporal information. Our objective was to use remotely sensed imagery to compare different vegetation indices as a means of assessing canopy variation and its resultant impact on corn (Zea mays L.) grain yield. Treatments consisted of five N rates and four hybrids, which were grown under irrigation near Shelton, NE on a Hord silt loam in 1997 and 1998. Imagery data with 0.5-m spatial resolution were collected from aircraft on several dates during both seasons using a multispectral, four-band [blue, green, red, and near-infrared reflectance] digital camera system. Imagery was imported into a geographical information system (GIS) and then geo-registered, converted into reflectance, and used to compute three vegetation indices. Grain yield for each plot was determined at maturity. Results showed that green normalized difference vegetation index (GNDVI) values derived from images acquired during midgrain filling were the most highly correlated with grain yield; maximum correlations were 0.7 and 0.92 in 1997 and 1998, respectively. Normalizing GNDVI and grain yield variability within hybrids improved the correlations in both years, but more dramatic increases were observed in 1997 (0.7 to 0.82) than in 1998 (0.92 to 0.95). This suggested GNDVI acquired during midgrain filling could be used to produce relative yield maps depicting spatial variability in fields, offering a potentially attractive alternative to use of a combine yield monitor

Assembling large, complex environmental metagenomes

The large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires significant computational resources. We apply two pre-assembly filtering approaches, digital normalization and partitioning, to make large metagenome assemblies more comput\ ationaly tractable. Using a human gut mock community dataset, we demonstrate that these methods result in assemblies nearly identical to assemblies from unprocessed data. We then assemble two large soil metagenomes from matched Iowa corn and native prairie soils. The predicted functional content and phylogenetic origin of the assembled contigs indicate significant taxonomic differences despite similar function. The assembly strategies presented are generic and can be extended to any metagenome; full source code is freely available under a BSD license

Tackling soil diversity with the assembly of large, complex metagenomes

The large volumes of sequencing data required to sample deeply the microbial communities of complex environments pose new challenges to sequence analysis. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires substantial computational resources. We combine two preassembly filtering approaches--digital normalization and partitioning--to generate previously intractable large metagenome assemblies. Using a human-gut mock community dataset, we demonstrate that these methods result in assemblies nearly identical to assemblies from unprocessed data. We then assemble two large soil metagenomes totaling 398 billion bp (equivalent to 88,000 Escherichia coli genomes) from matched Iowa corn and native prairie soils. The resulting assembled contigs could be used to identify molecular interactions and reaction networks of known metabolic pathways using the Kyoto Encyclopedia of Genes and Genomes Orthology database. Nonetheless, more than 60% of predicted proteins in assemblies could not be annotated against known databases. Many of these unknown proteins were abundant in both corn and prairie soils, highlighting the benefits of assembly for the discovery and characterization of novelty in soil biodiversity. Moreover, 80% of the sequencing data could not be assembled because of low coverage, suggesting that considerably more sequencing data are needed to characterize the functional content of soil

Tackling soil diversity with the assembly of large, complex metagenomes

The large volumes of sequencing data required to sample deeply the microbial communities of complex environments pose new challenges to sequence analysis. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires substantial computational resources. We combine two preassembly filtering approaches—digital normalization and partitioning—to generate previously intractable large metagenome assemblies. Using a human-gut mock community dataset, we demonstrate that these methods result in assemblies nearly identical to assemblies from unprocessed data. We then assemble two large soil metagenomes totaling 398 billion bp (equivalent to 88,000 Escherichia coli genomes) from matched Iowa corn and native prairie soils. The resulting assembled contigs could be used to identify molecular interactions and reaction networks of known metabolic pathways using the Kyoto Encyclopedia of Genes and Genomes Orthology database. Nonetheless, more than 60% of predicted proteins in assemblies could not be annotated against known databases. Many of these unknown proteins were abundant in both corn and prairie soils, highlighting the benefits of assembly for the discovery and characterization of novelty in soil biodiversity. Moreover, 80% of the sequencing data could not be assembled because of low coverage, suggesting that considerably more sequencing data are needed to characterize the functional content of soil