Sorcerer II: The Search for Microbial Diversity Roils the Waters

This feature explores bioprospecting and the legal issues related to collecting and cataloging microbial diversity from oceanic locations around the world

New insights into microbial ecology through subtle nucleotide variation

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 1318, doi:10.3389/fmicb.2016.01318.Characterizing the community structure of naturally occurring microbes through marker gene amplicons has gained widespread acceptance for profiling microbial populations. The 16S ribosomal RNA (rRNA) gene provides a suitable target for most studies since (1) it meets the criteria for robust markers of evolution, e.g., both conserved and rapidly evolving regions that do not undergo horizontal gene transfer, (2) microbial ecologists have identified widely adopted primers and protocols for generating amplicons for sequencing, (3) analyses of both cultivars and environmental DNA have generated well-curated databases for taxonomic profiling, and (4) bioinformaticians and computational biologists have published comprehensive software tools for interpreting the data and generating publication-ready figures. Since the initial descriptions of high-throughput sequencing of 16S rRNA gene amplicons to survey microbial diversity, we have witnessed an explosion of association-based inferences of interactions between microbes and their environment.AME was supported by the University of Chicago and the Marine Biological Laboratory collaboration award

Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents

Author Posting. © The Author(s), 2014. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in FEMS Microbiology Ecology 91 (2015): 1-11, doi:10.1093/femsec/fiu016.Environmental gradients generate countless ecological niches in deep-sea hydrothermal vent systems, which foster diverse microbial communities. The majority of distinct microbial lineages in these communities occur in very low abundance. However, the ecological role and distribution of rare and abundant lineages, particularly in deep, hot subsurface environments, remains unclear. Here, we use 16S rRNA tag sequencing to describe biogeographic patterning and microbial community structure of both rare and abundant archaea and bacteria in hydrothermal vent systems. We show that while rare archaeal lineages and almost all bacterial lineages displayed geographically restricted community structuring patterns, the abundant lineages of archaeal communities displayed a much more cosmopolitan distribution. Finally, analysis of one high-volume, high-temperature fluid sample representative of the deep hot biosphere described a unique microbial community that differed from microbial populations in diffuse flow fluid or sulfide samples, yet the rare thermophilic archaeal groups showed similarities to those that occur in sulfides. These results suggest that while most archaeal and bacterial lineages in vents are rare and display a highly regional distribution, a small percentage of lineages, particularly within the archaeal domain, are successful at widespread dispersal and colonization.Funding for this work was provided by a grant from the NASA Astrobiology Institute to the Carnegie Institution of Washington.2015-12-0

PENGARUH PENGETAHUAN AKUNTANSI, SKALA USAHA DAN PENGALAMAN USAHA TERHADAP PENGGUNAAN INFORMASI AKUNTANSI PADA UMKM DI KECAMATAN PONOROGO

Penelitian ini bertujuan untuk mengetahui pengaruh pengetahuan akuntansi, skala usaha dan pengalaman usaha terhadap penggunaan informasi akuntansi pelaku UMKM di Kecamatan Ponorogo. Adapun yang menjadi rumusan masalah dalam penelitian ini adalah Apakah pengetahuan akuntansi, skala usaha dan pengalaman usaha secara partial maupun simultan berpengaruh terhadap penggunaan informasi akuntansi pada pelaku UMKM di Kecamatan Ponorogo?. Populasi dalam penelitian ini adalah pelaku UMKM yang terdaftar di Kecamatan Ponorogo Kabupaten Ponorogo. Teknik sampling yang digunakan oleh peneliti adalah metode Cluster Random Sampling. Data yang diambil untuk melakukan penelitian ini adalah data primer dengan menggunakan instrumen kuesioner. Pengujian analisis kualitas data digunakan uji validitas dan uji reliabilitas. Kemudian untuk pengujian hipotesis menggunakan uji koefisien regresi secara persial (uji t), uji signifikansi simultan, dan koefisien determinan. Metode analisis data yang digunakan adalah regresi linier berganda. Hasil dari penelitian ini menunjukkan bahwa secara parsial (1) Pengetahuan akuntansi berpengaruh positif dan signifikan terhadap penggunaan informasi akuntansi pelaku UMKM Kecamatan Ponorogo. Hal tersebut menunjukkan bahwa sebagian besar menganggap pengetahuan akuntansi dalam kegiatan usaha akan mempengaruhi penggunaan informasi akuntansi; (2) Skala usaha berpengaruh positif dan signifikan terhadap Penggunaan Informasi Akuntansi pelaku UMKM Kecamatan Ponorogo. Hal tersebut menunjukkan bahwa sebagian besar menganggap skala usaha dalam kegiatan usaha akan mempengaruhi penggunaan informasi akuntansi; (3) Pengalaman usaha berpengaruh positif dan signifikan terhadap Penggunaan Informasi Akuntansi pelaku UMKM Kecamatan Ponorogo. Hal tersebut berarti sebagian besar menganggap pengalaman usaha dalam kegiatan usaha akan mempengaruhi penggunaan informasi akuntansi. Kemudian secara simultan menunjukkan bahwa Pengetahuan akuntansi, skala usaha dan pengalaman usaha berpengaruh positif dan signifikan terhadap Penggunaan Informasi Akuntansi pelaku UMKM Kecamatan Ponorogo

DRISEE overestimates errors in metagenomic sequencing data

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Briefings in Bioinformatics 15 (2014): 783-787, doi:10.1093/bib/bbt010.The extremely high error rates reported by Keegan et al. in ‘A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE’ (PLoS Comput Biol 2012;8:e1002541) for many next-generation sequencing datasets prompted us to re-examine their results. Our analysis reveals that the presence of conserved artificial sequences, e.g. Illumina adapters, and other naturally occurring sequence motifs accounts for most of the reported errors. We conclude that DRISEE reports inflated levels of sequencing error, particularly for Illumina data. Tools offered for evaluating large datasets need scrupulous review before they are implemented.National Institutes of Health [1UH2DK083993 to M.L.S.]; National Science Foundation [BDI- 096026 to S.M.H.]

The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing

© 2008 Author et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in PLoS Biology 6 (2008): e280, doi:10.1371/journal.pbio.0060280.The intestinal microbiota is essential to human health, with effects on nutrition, metabolism, pathogen resistance, and other processes. Antibiotics may disrupt these interactions and cause acute disease, as well as contribute to chronic health problems, although technical challenges have hampered research on this front. Several recent studies have characterized uncultured and complex microbial communities by applying a new, massively parallel technology to obtain hundreds of thousands of sequences of a specific variable region within the small subunit rRNA gene. These shorter sequences provide an indication of diversity. We used this technique to track changes in the intestinal microbiota of three healthy humans before and after treatment with the antibiotic ciprofloxacin, with high sensitivity and resolution, and without sacrificing breadth of coverage. Consistent with previous results, we found that the microbiota of these individuals was similar at the genus level, but interindividual differences were evident at finer scales. Ciprofloxacin reduced the diversity of the intestinal microbiota, with significant effects on about one-third of the bacterial taxa. Despite this pervasive disturbance, the membership of the communities had largely returned to the pretreatment state within 4 weeks

Life in the Dark: Phylogenetic and Physiological Diversity of Chemosynthetic Symbioses

Possibly the last discovery of a previously unknown major ecosystem on Earth was made just over half a century ago, when researchers found teaming communities of animals flourishing two and a half kilometers below the ocean surface at hydrothermal vents. We now know that these highly productive ecosystems are based on nutritional symbioses between chemosynthetic bacteria and eukaryotes and that these chemosymbioses are ubiquitous in both deep-sea and shallow-water environments. The symbionts are primary producers that gain energy from the oxidation of reduced compounds, such as sulfide and methane, to fix carbon dioxide or methane into biomass to feed their hosts. This review outlines how the symbiotic partners have adapted to living together. We first focus on the phylogenetic and metabolic diversity of these symbioses and then highlight selected research directions that could advance our understanding of the processes that shaped the evolutionary and ecological success of these associations

Identification of specialists and abundance-occupancy relationships among intestinal bacteria of Aves, Mammalia, and Actinopterygii

Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 82 (2016): 1496-1503, doi:10.1128/AEM.02456-15.The coalescence of next generation DNA sequencing methods, ecological perspectives, and bioinformatics analysis tools is rapidly advancing our understanding of the evolution and function of vertebrate-associated bacterial communities. Delineating host-microbial associations has applied benefits ranging from clinical treatments to protecting our natural waters. Microbial communities follow some broad-scale patterns observed for macro-organisms, but it remains unclear how specialization of intestinal vertebrate-associated communities to a particular host environment influences broad-scale patterns in microbial abundance and distribution. We analyzed the V6 region of 16S rRNA gene amplified from 106 fecal samples spanning Aves, Mammalia, and Actinopterygii (ray-finned fish). The interspecific abundance-occupancy relationship—where widespread taxa tend to be more abundant than narrowly distributed taxa—among operational taxonomic units (OTUs) was investigated within and among host species. In a separate analysis, specialists OTUs that were highly abundant in a single host and rare in all other hosts were identified using a multinomial model without excluding under-sampled OTUs a priori. We also show that intestinal microbes in humans and other vertebrates studied follow a similar interspecific abundance-occupancy relationship compared to plants and animals, as well as microbes in ocean and soil environments; but because intestinal host-associated communities have undergone intense specialization, this trend is violated by a disproportionately large number of specialist taxa. Although it is difficult to distinguish the effects of dispersal limitations, host selection, historical contingency, and stochastic processes on community assembly, results suggest bacterial taxa can be shared among diverse vertebrate hosts in ways similar to those of ‘free-living’ bacteria