Joy Van Nostrand | Utah State University (original) (raw)

Papers by Joy Van Nostrand

Adam P. Arkin* (aparkin@lbl.gov), Terry C. Hazen,* Carl Abulencia, Eric J. Alm, Gary Anderson, Ma... more Adam P. Arkin* (aparkin@lbl.gov), Terry C. Hazen,* Carl Abulencia, Eric J. Alm, Gary Anderson, Manfred Auer, Edward Baidoo, Kelly S. Bender, Peter Benke, Sharon Borglin, Eoin Brodie, Steven Brown, Lauren Camp, Romy Chakraborty, Swapnil Chhabra, Gabriela Chirica, Dylan Chivian, Michael Cipriano, Paramvir S. Dehal, Todd DeSantis, Elliot Drury, Inna Dubchak, Dwayne Elias, Matthew W. Fields, Veronica On Yi Fok, Julian Fortney, Sara Gaucher, Jil Geller, Masood Hadi, Zhili He, Chris Hemme, Kristina Hillesland, HoiYing Holman, Katherine H. Huang, Y. Wayne Huang, Chiachi Hwang, Janet Jacobsen, Marcin P. Joachimiak, Dominique Joyner, Jay Keasling, Keith Keller, Kimberly L. Keller, Martin Keller, Yooli Light, Eric Luning, Robert Meagher, Aindrila Mukhopadhyay, Anthony Palumbo, Richard Phan, Tommy Phelps, Francesco Pingitore, Mircea Podar, Morgan N. Price, Alyssa Redding, Jarrod Robertson, Rajat Sapra, Christopher Schadt, Matthew Shirley, Amy Shutkin, Mary Singer, Anup Singh, David A. Stahl, S...

Aindrila Mukhopadhyay,1,6* Edward Baidoo,1,6 Kelly Bender5,6 (bender@micro.siu.edu), Peter Benke,... more Aindrila Mukhopadhyay,1,6* Edward Baidoo,1,6 Kelly Bender5,6 (bender@micro.siu.edu), Peter Benke,1,6 Swapnil Chhabra,1,6 Elliot Drury,3,6 Masood Hadi,2,6 Zhili He,4,6 Jay Keasling1,6 (keasling@.berkeley.edu), Kimberly Keller,3,6 Eric Luning,1,6 Francesco Pingitore,1,6 Alyssa Redding,1,6 Jarrod Robertson,3,6 Rajat Sapra,2,6 Anup Singh2,6 (aksingh@sandia.gov), Judy Wall3,6 (wallj@ missouri.edu), Grant Zane,3,6 Aifen Zhou,4,6 and Jizhong Zhou4,6 (jzhou@rccc.ou.edu)

WEI-MIN WU, JACK CARLEY, JIAN LUO, MATTHEW A GINDER-VOGEL, ERICK 4 CARDENAS, MARY BETH LEIGH, CHA... more WEI-MIN WU, JACK CARLEY, JIAN LUO, MATTHEW A GINDER-VOGEL, ERICK 4 CARDENAS, MARY BETH LEIGH, CHAICHI HWANG, SHELLY D. KELLY, CHAUNGMIN 5 RUAN, LIYOU WU, JOY VAN NOSTRAND, TERRY GENTRY , KENNETH LOWE, TONIA 6 MEHLHORN, SUE CARROLL, WENSUI LOU, MATTHEW W. FIELDS, BAOHUA GU, 7 DAVID WATSON, KENNETH M. KEMNER, TERENCE MARSH, JAMES TIEDJE, JIZHONG 8 ZHOU, SCOTT FENDORF, PETER K. KITANIDIS, PHILIP M. JARDINE, AND CRAIG S. 9 CRIDDLE 10

Background: Bacterial predation is an important selective force in microbial community structure ... more Background: Bacterial predation is an important selective force in microbial community structure and dynamics. However, only a limited number of predatory bacteria have been reported, and their predatory strategies and evolutionary adaptations remain elusive. We recently isolated a novel group of bacterial predators, Bradymonabacteria, representative of the novel order Bradymonadales in δ- Proteobacteria . Compared with those of other bacterial predators (e.g., Myxococcales and Bdellovibrionales ), the predatory and living strategies of Bradymonadales are still largely unknown. Results: Based on individual coculture of Bradymonabacteria with 281 prey bacteria, Bradymonabacteria preyed on diverse bacteria but had a high preference for Bacteroidetes . Genomic analysis of 13 recently sequenced Bradymonabacteria indicated that these bacteria had conspicuous metabolic deficiencies, but they could synthesize many polymers, such as polyphosphate and polyhydroxyalkanoates. Dual-transcriptom...

mBio, Feb 20, 2018

Contamination from anthropogenic activities has significantly impacted Earth's biosphere. How... more Contamination from anthropogenic activities has significantly impacted Earth's biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN), representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate) increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not ni...

Frontiers in microbiology, 2017

Diazotrophic communities make an essential contribution to the productivity through providing new... more Diazotrophic communities make an essential contribution to the productivity through providing new nitrogen. However, knowledge of the roles that both mangrove tree species and geochemical parameters play in shaping mangove rhizosphere diazotrophic communities is still elusive. Here, a comprehensive examination of the diversity and structure of microbial communities in the rhizospheres of three mangrove species, Rhizophora apiculata, Avicennia marina, and Ceriops tagal, was undertaken using high-throughput sequencing of the 16S rRNA and nifH genes. Our results revealed a great diversity of both the total microbial composition and the diazotrophic composition specifically in the mangrove rhizosphere. Deltaproteobacteria and Gammaproteobacteria were both ubiquitous and dominant, comprising an average of 45.87 and 86.66% of total microbial and diazotrophic communities, respectively. Sulfate-reducing bacteria belonging to the Desulfobacteraceae and Desulfovibrionaceae were the dominant d...

Frontiers in Microbiology

The coral holobiont often resides in oligotrophic waters; both coral cells and their symbiotic di... more The coral holobiont often resides in oligotrophic waters; both coral cells and their symbiotic dinoflagellates possess ammonium assimilation enzymes and potentially benefit from the nitrogen fixation of coral-associated diazotrophs. However, the seasonal dynamics of coral-associated diazotrophs are not well characterized. Here, the seasonal variations of diazotrophic communities associated with three corals, Galaxea astreata, Pavona decussata, and Porites lutea, were studied using nifH gene amplicon pyrosequencing techniques. Our results revealed a great diversity of coral-associated diazotrophs. nifH sequences related to Alphaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria were ubiquitous and dominant in all corals in two seasons. In contrast with the coral P. decussata, both G. astreata and P. lutea showed significant seasonal changes in the diazotrophic communities and nifH gene abundance. Variable diazotroph groups accounted for a range from 11 to 49% within individual coral samples. Most of the variable diazotrophic groups from P. decussata were speciesspecific, however, the majority of overlapping variable groups in G. astreata and P. lutea showed the same seasonal variation characteristics. Rhodopseudomonas palustris-and Gluconacetobacter diazotrophicus-affiliated sequences were relatively abundant in the summer, whereas a nifH sequence related to Halorhodospira halophila was relatively abundant in spring G. astreata and P. lutea. The seasonal variations of all diazotrophic communities were significantly correlated with the seasonal shifts of ammonium and nitrate, suggesting that diazotrophs play an important role in the nitrogen cycle of the coral holobiont.

FEMS Microbiology Ecology

The potential for modern coalfield methanogenesis was assessed using formation water as inocula i... more The potential for modern coalfield methanogenesis was assessed using formation water as inocula in nutrient-replete incubations amended with presumed intermediates of anaerobic coal biodegradation.

Journal of hazardous materials, Jan 2, 2017

Increased amount of nano-silver will be released into domestic and industrial waste streams due t... more Increased amount of nano-silver will be released into domestic and industrial waste streams due to its extensive application. However, great controversy still exists on the effects of silver nanoparticle (Ag-NP) on biological wastewater treatment processes and a toxicology model has not been built yet. Four sequencing batch reactors with activated sludge has been run for over three months with different silver species at a concentration of 1mg Ag/L in influent. Both freshly prepared Ag-NPs and aged Ag-NPs were tested with released silver ion as control. Results in this study showed that Ag-NPs, especially freshly prepared Ag-NPs, can help to maintain or even increase the diversity of microbial community in activated sludge and the biomass concentration even under long-term treatment. It indicates that the hormesis model need to be considered for the toxicology of Ag-NPs.

Molecular ecology, Jan 24, 2017

Uncovering which environmental factors govern community diversity patterns and how ecological pro... more Uncovering which environmental factors govern community diversity patterns and how ecological processes drive community turnover are key questions related to understand the community assembly. However, the ecological mechanisms regulating long-term variations of bacterioplankton communities in lake ecosystems remains poorly understood. Here we present nearly a decade-long study of bacterioplankton communities from the eutrophic Lake Donghu (Wuhan, China) using 16S rRNA gene amplicon sequencing with MiSeq platform. We found strong repeatable seasonal diversity patterns in terms of both common (detected in more than 50% samples) and dominant (relative abundance > 1%) bacterial taxa turnover. Moreover, community composition tracked the seasonal temperature gradient, indicating that temperature is an key environmental factor controlling observed diversity patterns. Total phosphorus also contributed significantly to the seasonal shifts in bacterioplankton composition. However, any spa...

Environmental science & technology, Apr 4, 2017

To further understand the diversity and dynamics of SRB in response to substrate amendment, we se... more To further understand the diversity and dynamics of SRB in response to substrate amendment, we sequenced genes coding for the dissimilatory sulfite reductase (dsrA) in groundwater samples collected after an emulsified vegetable oil (EVO) amendment, which sustained U(VI)-reducing conditions for one year in a fast-flowing aquifer. EVO amendment significantly altered the composition of groundwater SRB communities. Sequences having no closely related-described species dominated (80%) the indigenous SRB communities in nonamended wells. After EVO amendment, Desulfococcus, Desulfobacterium, and Desulfovibrio, known for long-chain-fatty-acid, short-chain-fatty-acid and H2 oxidation and U(VI) reduction, became dominant accounting for 7 ± 2%, 21 ± 8%, and 55 ± 8% of the SRB communities, respectively. Succession of these SRB at different bioactivity stages based on redox substrates/products (acetate, SO4(-2), U(VI), NO3(-), Fe(II), and Mn(II)) was observed. Desulfovibrio and Desulfococcus domi...

mBio, 2016

ABSTRACTClipping (i.e., harvesting aboveground plant biomass) is common in agriculture and for bi... more ABSTRACTClipping (i.e., harvesting aboveground plant biomass) is common in agriculture and for bioenergy production. However, microbial responses to clipping in the context of climate warming are poorly understood. We investigated the interactive effects of grassland warming and clipping on soil properties and plant and microbial communities, in particular, on microbial functional genes. Clipping alone did not change the plant biomass production, but warming and clipping combined increased the C4peak biomass by 47% and belowground net primary production by 110%. Clipping alone and in combination with warming decreased the soil carbon input from litter by 81% and 75%, respectively. With less carbon input, the abundances of genes involved in degrading relatively recalcitrant carbon increased by 38% to 137% in response to either clipping or the combined treatment, which could weaken long-term soil carbon stability and trigger positive feedback with respect to warming. Clipping alone al...

Frontiers in Microbiology, 2016

The McMurdo Dry Valleys of Antarctica are an extreme polar desert. Mineral soils support subsurfa... more The McMurdo Dry Valleys of Antarctica are an extreme polar desert. Mineral soils support subsurface microbial communities and translucent rocks support development of hypolithic communities on ventral surfaces in soil contact. Despite significant research attention, relatively little is known about taxonomic and functional diversity or their interrelationships. Here we report a combined diversity and functional interrogation for soil and hypoliths of the Miers Valley in the McMurdo Dry Valleys of Antarctica. The study employed 16S rRNA fingerprinting and high throughput sequencing combined with the GeoChip functional microarray. The soil community was revealed as a highly diverse reservoir of bacterial diversity dominated by actinobacteria. Hypolithic communities were less diverse and dominated by cyanobacteria. Major differences in putative functionality were that soil communities displayed greater diversity in stress tolerance and recalcitrant substrate utilization pathways, whilst hypolithic communities supported greater diversity of nutrient limitation adaptation pathways. A relatively high level of functional redundancy in both soil and hypoliths may indicate adaptation of these communities to fluctuating environmental conditions.

Frontiers in microbiology, 2016

The elevational and latitudinal diversity patterns of microbial taxa have attracted great attenti... more The elevational and latitudinal diversity patterns of microbial taxa have attracted great attention in the past decade. Recently, the distribution of functional attributes has been in the spotlight. Here, we report a study profiling soil microbial communities along an elevation gradient (500-2200 m) on Changbai Mountain. Using a comprehensive functional gene microarray (GeoChip 5.0), we found that microbial functional gene richness exhibited a dramatic increase at the treeline ecotone, but the bacterial taxonomic and phylogenetic diversity based on 16S rRNA gene sequencing did not exhibit such a similar trend. However, the β-diversity (compositional dissimilarity among sites) pattern for both bacterial taxa and functional genes was similar, showing significant elevational distance-decay patterns which presented increased dissimilarity with elevation. The bacterial taxonomic diversity/structure was strongly influenced by soil pH, while the functional gene diversity/structure was sign...

Oklahoma Water Resources Research Institute, 2012

Bioresource technology, 2015

Methane (CH4) is a readily available feedstock for production of polyhydroxyalkanoates (PHAs). Th... more Methane (CH4) is a readily available feedstock for production of polyhydroxyalkanoates (PHAs). The structure and PHA production capacity of a Methylocystis-dominated methanotrophic enrichment was stable in long-term operation (>175days) when grown exponentially under non-aseptic conditions in fill-and-draw batch cultures with ammonium as nitrogen source. Cells harvested in the draw step were incubated in the absence of nitrogen with various combinations of CH4 and valerate to assess capacity for synthesis of poly(3-hydroxybutyrate) (P3HB) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). When fed CH4 alone, only P3HB was produced. When fed CH4 plus valerate, PHBV was synthesized. The mol% of 3-hydroxyvalerate (3HV) increased with added valerate. Oxidation of CH4 was required for valerate assimilation, and the fraction of CH4 oxidized increased with increased mol% 3HV. By separating PHA accumulation from cell replication, tailored PHA-rich biomass can be generated by additi...

The global atmospheric concentration of CO2 has increased by more than 30percent since the indust... more The global atmospheric concentration of CO2 has increased by more than 30percent since the industrial revolution. Although the stimulating effects of elevated CO2 (eCO2) on plant growth and primary productivity have been well studied, its influences on belowground microbial communities are poorly understood and controversial. In this study, we showed a significant change in the structure and functional potential of soil microbial communities at eCO2 in a grassland ecosystem, the BioCON (Biodiversity, CO2 and Nitrogen) experimental site (http://www.biocon.umn.edu/) using a comprehensive functional gene array, GeoChip 3.0, which contains about 28,0000 probes and covers approximately 57,000 gene variants from 292 functional gene families involved in carbon, nitrogen, phosphorus and sulfur cycles as well as other functional processes. GeoChip data indicated that the functional structure of microbial communities was markedly different between ambient CO2 (aCO2) and eCO2 by detrended corr...

PLOS ONE, 2015

Biosynthesis of the popular dyestuff indigo from indole has been comprehensively studied using pu... more Biosynthesis of the popular dyestuff indigo from indole has been comprehensively studied using pure cultures, but less has been done to characterize the indigo production by microbial communities. In our previous studies, a wild strain Comamonas sp. MQ was isolated from activated sludge and the recombinant Escherichia coli nagAc carrying the naphthalene dioxygenase gene (nag) from strain MQ was constructed, both of which were capable of producing indigo from indole. Herein, three activated sludge systems, G1 (non-augmented control), G2 (augmented with Comamonas sp. MQ), and G3 (augmented with recombinant E. coli nagAc), were constructed to investigate indigo production. After 132-day operation, G3 produced the highest yields of indigo (99.5 ± 3.0 mg/l), followed by G2 (27.3 ± 1.3 mg/l) and G1 (19.2 ± 1.2 mg/l). The microbial community dynamics and activities associated with indigo production were analyzed by Illumina Miseq sequencing of 16S rRNA gene amplicons. The inoculated strain MQ survived for at least 30 days, whereas E. coli nagAc was undetectable shortly after inoculation. Quantitative real-time PCR analysis suggested the abundance of naphthalene dioxygenase gene (nagAc) from both inoculated strains was strongly correlated with indigo yields in early stages (0-30 days) (P < 0.001) but not in later stages (30-132 days) (P > 0.10) of operation. Based on detrended correspondence analysis (DCA) and dissimilarity test results, the communities underwent a noticeable shift during the operation. Among the four major genera (> 1% on average), the commonly reported indigo-producing populations Comamonas and Pseudomonas showed no positive relationship with indigo yields (P > 0.05) based on Pearson correlation test, while Alcaligenes and Aquamicrobium, rarely reported for indigo production, were positively correlated with indigo yields (P < 0.05). This study should provide new insights into our understanding of indigo bio-production by microbial communities.

Chemosphere, 2015

We studied functional diversity of a heavy metal polluted soil under phytoremediation. Soils reme... more We studied functional diversity of a heavy metal polluted soil under phytoremediation. Soils remediated with willow trees short rotations were compared to a grassland soil. Functional diversity and activities were higher in remediated than in grassland soil.

BMC Microbiology, 2015

Background: Although high-throughput sequencing, such as Illumina-based technologies (e.g. MiSeq)... more Background: Although high-throughput sequencing, such as Illumina-based technologies (e.g. MiSeq), has revolutionized microbial ecology, adaptation of amplicon sequencing for environmental microbial community analysis is challenging due to the problem of low base diversity. Results: A new phasing amplicon sequencing approach (PAS) was developed by shifting sequencing phases among different community samples from both directions via adding various numbers of bases (0-7) as spacers to both forward and reverse primers. Our results first indicated that the PAS method substantially ameliorated the problem of unbalanced base composition. Second, the PAS method substantially improved the sequence read base quality (an average of 10 % higher of bases above Q30). Third, the PAS method effectively increased raw sequence throughput (~15 % more raw reads). In addition, the PAS method significantly increased effective reads (9-47 %) and the effective read sequence length (16-96 more bases) after quality trim at Q30 with window 5. In addition, the PAS method reduced half of the sequencing errors (0.54-1.1 % less). Finally, two-step PCR amplification of the PAS method effectively ameliorated the amplification biases introduced by the long barcoded PCR primers. Conclusion: The developed strategy is robust for 16S rRNA gene amplicon sequencing. In addition, a similar strategy could also be used for sequencing other genes important to ecosystem functional processes