Biology subjects

Scott, J. J.

Publications and source records attributed to Scott, J. J..

3 recordsLinked to original sources

bioRxiv2018

A genus definition for Bacteria and Archaea based on genome relatedness and taxonomic affiliation.

Genus assignment is fundamental in the characterization of microbes, yet there is currently no unambiguous way to demarcate genera solely using standard genomic relatedness indices. Here, we propose an approach to demarcate genera that relies on the combined use of the average nucleotide identity, genome alignment fraction, and the distinction between type species and non-type species. More than 750 genomes representing type strains of species from 10 different phyla, and 19 different taxonomic orders/families in Gram-positive/negative, bacterial and archaeal lineages were tested. Overall, all 19 analyzed taxa conserved significant genomic differences between members of a genus and type species of other genera in the same taxonomic family. Bacillus, Flavobacterium, Hydrogenovibrio, Lactococcus, Methanosarcina, Thiomicrorhabdus, Thiomicrospira, Shewanella, and Vibrio are discussed in detail. Less than 1% of the type strains analyzed need reclassification, highlighting that the adoption of the 16S rRNA gene as a taxonomic marker has provided consistency to the classification of microorganisms in recent decades. One exception to this is the genus Bacillus with 61% of type strains needing reclassification, including the human pathogens B. cereus and B. anthracis. The results provide a first line of evidence that the combination of genomic indices provides appropriate resolution to effectively demarcate genera within the current taxonomic framework that is based on the 16S rRNA gene. We also identify the emergence of natural breakpoints at the genome level that can further help in the circumscription of genera. Altogether, these results show that a distinct difference between distant relatives and close relatives at the genome level (i.e., genomic coherence) is an emergent property of genera in Bacteria and Archaea.

microbiology↗

bioRxiv2017

A biological source of marine sedimentary iron oxides

The biogeochemical cycle of iron is intricately linked to numerous element cycles. Although reductive biological processes that bridge the iron cycle to other element cycles are established, little is known about microbial oxidative processes on iron cycling in sedimentary environments--resulting in the formation of iron oxides. Here, we show that a major source of sedimentary iron oxides originates from the metabolic activity of iron-oxidizing bacteria from the class Zetaproteobacteria, stimulated by burrowing animals in coastal sediments. Zetaproteobacteria were estimated to be a global total of 1026 cells in coastal, bioturbated sediments and would equate to an annual production of approximately 7.9 x 1015 grams of sedimentary iron oxides--twenty-five times larger than the annual flux of iron oxides by rivers. These data suggest that iron-oxidizing Zetaproteobacteria are keystone organisms in marine sedimentary environments given their low numerical abundance; yet exert a profound impact via the production of iron oxides.

microbiology↗

bioRxiv2016

In situ estimates of iron-oxidation and accretion rates for iron-oxidizing bacterial mats at Loihi Seamount.

It is increasingly recognized that diffuse, hydrothermal venting is an important source of iron to the deep-sea that can influence oceanic iron dynamics and abundance. Lithotrophic Fe-oxidizing bacteria (FeOB) are dominant at diffuse hydrothermal vent sites, producing microbial iron mats that are often centimeters or more thick. At present, little is known about in situ Fe-oxidation rates, or accretion rates for iron mats. An in situ productivity chamber was developed that took advantage of the unique mineral morphotypes produced by FeOB to estimate rates of Fe-oxidation and accretion. Chambers were placed at two diffuse vents (1179 and 1300 mbsl) at L[o]ihi Seamount where they were colonized by FeOB for different amounts of time. From this analysis, it was estimated that Fe-oxidation rates could range from 8.2-51.9 x 10-6 mol {middle dot} hr-1, and that iron mats could accrete at around 2.2 cm {middle dot} yr-1. Molecular analysis indicated that the relative abundance of Zetaproteobacteria, a group of known FeOB, accounted for 80-90% of the bacteria colonizing the chambers. There was a distinct difference between populations at the 1179m site (Pohaku), and the 1300m site (North Hiolo Ridge). Microscope slides placed within the productivity chambers were colonized by different morphotypes of FeOB. The cells responsible for one common morphotype that produces a Y-shaped filament were identified as Zetaproteobacteria by use of a small subunit rRNA probe. This work confirms the importance of FeOB in the formation of chemosynthetic iron mats, and provides the first estimates for in situ Fe-oxidation rates and mat accretion rates.\n\nHighlightsO_LIAn in-situ productivity chamber was developed to estimate rates of Fe-oxidation and understand colonization patterns at chemosynthetic iron mats at L[o]ihi Seamount.\nC_LIO_LIFe-oxidation rates ranged from 8.2-51.9 x 10-6 mol {dot} hr-1, and it was estimated that the iron mats could accrete at around 2.2 cm {dot} yr-1.\nC_LIO_LIThe iron mat community was dominated by Zetaproteobacteria, whose relative abundance accounted for up to 89% of the microbial community.\nC_LIO_LIThe community membership that grew during short-term incubations reflected the community composition of nearby microbial mats.\nC_LI

microbiology↗