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At least 955 records · Page 53

Effects of Bioreactor Retention Time on Aerobic Microbial Decomposition of CELSS Crop Residues

The focus of resource recovery research at the KSC-CELSS Breadboard Project has been the evaluation of microbiologically mediated biodegradation of crop residues by manipulation of bioreactor process and environmental variables. We will present results from over 3 years of studies that used laboratory- and breadboard-scale (8 and 120 L working volumes, respectively) aerobic, fed-batch, continuous stirred tank reactors (CSTR) for recovery of carbon and minerals from breadboard grown wheat and white potato residues. The paper will focus on the effects of a key process variable, bioreactor retention time, on response variables indicative of bioreactor performance. The goal is to determine the shortest retention time that is feasible for processing CELSS crop residues, thereby reducing bioreactor volume and weight requirements. Pushing the lower limits of bioreactor retention times will provide useful data for engineers who need to compare biological and physicochemical components. Bioreactor retention times were manipulated to range between 0.25 and 48 days. Results indicate that increases in retention time lead to a 4-fold increase in crop residue biodegradation, as measured by both dry weight losses and CO2 production. A similar overall trend was also observed for crop residue fiber (cellulose and hemicellulose), with a noticeable jump in cellulose degradation between the 5.3 day and 10.7 day retention times. Water-soluble organic compounds (measured as soluble TOC) were appreciably reduced by more than 4-fold at all retention times tested. Results from a study of even shorter retention times (down to 0.25 days), in progress, will also be presented.

Strayer, R. F.↗

Surveying Grassland Islands: the genetics and performance of Appalachian switchgrass (Panicum virgatum L.) collections

The interior Southeastern United States could contain novel germplasm for the bioenergy crop switchgrass due to its diverse habitats and geographic location between genetic subpopulations (Atlantic, Midwest, and Gulf). Collections from this region could accelerate breeding progress, contribute to conservation efforts, and improve understanding of isolated grasslands in the region. This study located 22 sites in the Midsouth region and obtained 1,521,210 single nucleotide polymorphism markers of 202 individuals through genotype-by-sequencing. Here, individuals were evaluated for flowering time, winter survival and tiller number. Comparison to a national diversity panel revealed that branches of two major subpopulations occur in the region with two levels of polyploidy: Atlantic tetraploids and Midwest octoploids. Two locations contained admixed octoploid individuals with Midwest and Gulf genetics. Field performance of the Midwest octoploids conformed with prior reported performance of the Midwest subpopulation, although three sites contained promising late flowering traits. The Atlantic tetraploids had moderate winter survival, short stature, and anomalously early flowering. Atlantic populations mostly occurred in marginal sites and their morphological and flowering time adaptations may be a resource conservation strategy. Demographic inference of historical effective population size variation in a subset of tetraploid locations indicated a widespread recent decline in effective population size. This pattern is consistent with isolation of these switchgrass communities from larger populations and is further supported by evidence of inbreeding within the populations (F I = 0.18). The populations documented in this study contain novel genetic diversity and adaptations to a range of marginal habitats. Therefore, this study provides a new source of germplasm for future breeding and conservation programs.

59 BASIC BIOLOGICAL SCIENCES↗

RefAHL: a curated quorum sensing reference linking diverse LuxI-type signal synthases with their acyl-homoserine lactone products

Some bacteria use acyl-homoserine lactone (AHL) signals in quorum sensing, a type of cell-cell communication. Here, we present “RefAHL,” an updated, curated collection of LuxI-type AHL synthases with their AHL products and associated metadata. RefAHL is publicly available as a community resource to help catalog LuxI-type diversity encoded in (meta) genomic data.

59 BASIC BIOLOGICAL SCIENCES↗

The Plant Microbiome: From Ecology to Reductionism and Beyond

Methodological advances over the past two decades have propelled plant microbiome research, allowing the field to comprehensively test ideas proposed over a century ago and generate many new hypotheses. Studying the distribution of microbial taxa and genes across plant habitats has revealed the importance of various ecological and evolutionary forces shaping plant microbiota. In particular, selection imposed by plant habitats strongly shapes the diversity and composition of microbiota and leads to microbial adaptation associated with navigating the plant immune system and utilizing plant-derived resources. Reductionist approaches have demonstrated that the interaction between plant immunity and the plant microbiome is, in fact, bidirectional and that plants, microbiota, and the environment shape a complex chemical dialogue that collectively orchestrates the plantmicrobiome. Finally, the next stage in plant microbiome research will require the integration of ecological and reductionist approaches to establish a general understanding of the assembly and function in both natural and managed environments.

59 BASIC BIOLOGICAL SCIENCES↗

The MELISSA pilot plant facility as as integration test-bed for advanced life support systems

The different advances in the Micro Ecological Life Support System Alternative project (MELISSA), fostered and coordinated by the European Space Agency, as well as in other associated technologies, are integrated and demonstrated in the MELISSA Pilot Plant laboratory. During the first period of operation, the definition of the different compartments at an individual basis has been achieved, and the complete facility is being re-designed to face a new period of integration of all these compartments. The final objective is to demonstrate the potentiality of biological systems such as MELISSA as life support systems. The facility will also serve as a test bed to study the robustness and stability of the continuous operation of a complex biological system. This includes testing of the associated instrumentation and control for a safe operation, characterization of the chemical and microbial safety of the system, as well as tracking the genetic stability of the microbial strains used. The new period is envisaged as a contribution to the further development of more complete biological life support systems for long-term manned missions, that should be better defined from the knowledge to be gained from this integration phase. This contribution summarizes the current status of the Pilot Plant and the planned steps for the new period. c2004 COSPAR. Published by Elsevier Ltd. All rights reserved.

Waste Management/instrumentation/methods↗

Assembly, comparative analysis, and utilization of a single haplotype reference genome for soybean

Cultivar Williams 82 has served as the reference genome for the soybean research community since 2008, but is known to have areas of genomic heterogeneity among different sub-lines. This work provides an updated assembly (version Wm82.a6) derived from a specific sub-line known as Wm82-ISU-01 (seeds available under USDA accession PI 704477). The genome was assembled using Pacific BioSciences HiFi reads and integrated into chromosomes using HiC. The 20 soybean chromosomes assembled into a genome of 1.01Gb, consisting of 36 contigs. The genome annotation identified 48 387 gene models, named in accordance with previous assembly versions Wm82.a2 and Wm82.a4. Comparisons of Wm82.a6 with other near-gapless assemblies of Williams 82 reveal large regions of genomic heterogeneity, including regions of differential introgression from the cultivar Kingwa within approximately 30 Mb and 25 Mb segments on chromosomes 03 and 07, respectively. Additionally, our analysis revealed a previously unknown large (> 20 Mb) heterogeneous region in the pericentromeric region of chromosome 12, where Wm82.a6 matches the ‘Williams’ haplotype while the other two near-gapless assemblies do not match the haplotype of either parent of Williams 82. In addition to the Wm82.a6 assembly, we also assembled the genome of ‘Fiskeby III,’ a rich resource for abiotic stress resistance genes. A genome comparison of Wm82.a6 with Fiskeby III revealed the nucleotide and structural polymorphisms between the two genomes within a QTL region for iron deficiency chlorosis resistance. The Wm82.a6 and Fiskeby III genomes described here will enhance comparative and functional genomics capacities and applications in the soybean community.

59 BASIC BIOLOGICAL SCIENCES↗

Quinoa Phenotyping Methodologies: An International Consensus

Quinoa is a crop originating in the Andes but grown more widely and with the genetic potential for significant further expansion. Due to the phenotypic plasticity of quinoa, varieties need to be assessed across years and multiple locations. To improve comparability among field trials across the globe and to facilitate collaborations, components of the trials need to be kept consistent, including the type and methods of data collected. Here, an internationally open-access framework for phenotyping a wide range of quinoa features is proposed to facilitate the systematic agronomic, physiological and genetic characterization of quinoa for crop adaptation and improvement. Mature plant phenotyping is a central aspect of this paper, including detailed descriptions and the provision of phenotyping cards to facilitate consistency in data collection. High-throughput methods for multi-temporal phenotyping based on remote sensing technologies are described. Tools for higher-throughput post-harvest phenotyping of seeds are presented. A guideline for approaching quinoa field trials including the collection of environmental data and designing layouts with statistical robustness is suggested. To move towards developing resources for quinoa in line with major cereal crops, a database was created. The Quinoa Germinate Platform will serve as a central repository of data for quinoa researchers globally.

59 BASIC BIOLOGICAL SCIENCES↗

How do we get from cell and animal data to risks for humans from space radiations?

After four decades of human exploration in space, many scientists consider the medical consequences from radiation exposures to be the major biological risk associated with long-term missions. This conclusion is based upon results from a research program that has evolved over the past thirty years. Despite the diversity in both opinions and approaches that necessarily arise in research endeavors such as this, a commonality has emerged from our community. We need epidemiological data for humans, animal data in areas where no human data exist, and data on mechanisms to get from animal to humans. We need a programmatic infrastructure that addresses specific goals as well as basic research. These concepts might be deemed overly simplistic and even tautologous were it not for the fact that they are frequently underutilized and even ignored. This article examines the goals, premises, and infrastructures proposed by expert panels and agencies to address radiation risks in space. It is proposed that the required level of effort and the resources available demand a unified, focused international effort that is, at the same time, subjected to rigorous peer review if it is to be successful. There is a plan; let us implement it.

Non-NASA Center↗

The membrane bioreactor (MBR): A hybrid technology for bioregenerative wastewater treatment and resource recovery in space

Extraplanetary surface habitat life support systems (LSS) on the Moon and Mars, as well as long-duration space travel, will require novel capabilities to withstand anticipated unique, harsh conditions. In order to provide safe, habitable environments for the crew, water purification and waste processing systems will be required to treat all sources of water (condensate, Sabatier, urine, hygiene, fecal, food waste) in order to achieve the necessary levels of recovery needed to sustain life over the long-duration missions. The ability to recycle organic wastes creates an opportunity to recover critical elements (e.g., C, H, O, N, P) for subsequent food production, water purification, and atmospheric regeneration. Bioregenerative systems mimic functions of nature in engineered systems, or bioreactors, utilizing combination of prokaryotes, eukaryotes and archaea. While these systems are commonly used on Earth for wastewater treatment, bioreactors for space travel face additional challenges. Terrestrial bioreactors often rely on gravitational settling of dense flocs and granules for cell retention. For micro- or partial-gravity environments, density differential alone will not be adequate for cell retention; a gravity-independent means for cell retention is crucial. The membrane bioreactor represents the state of the art in wastewater treatment. This hybrid system combines biological processes with membrane filtration to achieve performance beyond what each can accomplish individually. The complete cell retention in an MBR allows for the decoupling of hydraulic retention time (HRT) and solids retention time (SRT), which result in a high-thruput, compact, treatment system. The Bioregenerative Water Technology Team at NASA Kennedy Space Center and the University of South Florida has developed a bioregenerative platform based on the hybrid MBR technology. The overall architecture is compact, modular, flexible, and adaptable to mission evolutions. The main subsystems of the bioregenerative architecture include: 1) Anaerobic membrane bioreactor (AnMBR): Also termed the Organic processor assembly (OPA), the function of the AnMBR is to treat organic wastes such as fecal and food wastes. These wastes are characterized by a concentration of suspended solids comprised of carbohydrates, proteins and lipids. The assigned function of the AnMBR is to break down and covert suspended solids to biogas (methane, hydrogen and carbon dioxide), reduce effluent chemical oxygen demand (COD), liberate organically-bound nutrients, and remove pathogenic organisms. 2) Phototrophic membrane bioreactor (PMBR): The PMBR is comprised of a co-culture of microalgae and bacteria. The assigned function of the PMBR is to polish the permeate of the AnMBR to further remove dissolved organic carbon, manage nutrients (nitrogen transformation, load dampening), and perform air revitalization. 3) Food processor assembly (FPA): The FPA is a food production platform (prokaryotic or eukaryotic), fueled by outputs from the AnMBR, or PMBR. For the presentation, we will describe each step of the bioregenerative architecture, and present performance data from extended trials treating analog and real metabolic wastes.

Bioreactor↗

Factors Affecting Bait Site Visitation: Area of Influence of Baits

Baiting is a fundamental strategy for the global management of wild pigs (Sus scrofa); however, little information exists on how anthropogenic bait affects wild pig movements on a landscape. We investigated factors that are important in determining the spatial area of attraction for wild pigs to bait (‘area of influence’ of a bait site) using data from Global Positioning System (GPS) collars and locations of bait sites. We monitored movements of wild pigs in 2 distinct study areas in the United States from February to September 2016 and used locational data using GPS collars to analyze the influence of habitat quality (dependent on site), home range size, number of bait sites in the home range, distance to a bait site, and sex in relation to movement in time and space. We determined the average area of influence by calculating the area of a circle with the radius as the average maximum distance travelled by wild pigs to reach a bait site. The average area of influence for our bait sites was 6.7 km 2 (or a radius of approximately 1.5 km), suggesting a bait spacing of approximately 1.5 km would be adequate to capture visitation by most wild pigs and a spacing of 3 km could allow substantial visitation while minimizing redundant effort depending on the spatial structure of the populations. Eighty percent of wild pigs first visited bait sites within 8.9 days after bait deployment; and they visited earlier when their home range size was larger. As the number of bait sites in an individual's home range increased, individual pigs visited more bait sites, and the probability of a visit increased dramatically up to approximately 5 bait sites and much less thereafter. Wild pigs travelled farther distances to visit bait sites in lower quality habitat. Our results support the hypothesis that habitat quality can mediate the efficacy of baiting programs for wildlife by influencing their movement patterns and motivation to use anthropogenic resources. Our results suggest wild pigs will travel extensively within their home range to visit bait sites, and that in lower quality habitat, most animals will find bait sites more quickly. Determining the area of influence of bait sites can increase the efficacy of planning and monitoring management programs. Overall, our study provides new information to help managers plan baiting designs to attract the greatest number of pigs.

59 BASIC BIOLOGICAL SCIENCES↗

Genome-Resolved Metaproteomics Decodes the Microbial and Viral Contributions to Coupled Carbon and Nitrogen Cycling in River Sediments

Rivers have a significant role in global carbon and nitrogen cycles, serving as a nexus for nutrient transport between terrestrial and marine ecosystems. Although rivers have a small global surface area, they contribute substantially to worldwide greenhouse gas emissions through microbially mediated processes within the river hyporheic zone. Despite this importance, research linking microbial and viral communities to specific biogeochemical reactions is still nascent in these sediment environments. To survey the metabolic potential and gene expression underpinning carbon and nitrogen biogeochemical cycling in river sediments, we collected an integrated data set of 33 metagenomes, metaproteomes, and paired metabolomes. We reconstructed over 500 microbial metagenome-assembled genomes (MAGs), which we dereplicated into 55 unique, nearly complete medium- and high-quality MAGs spanning 12 bacterial and archaeal phyla. We also reconstructed 2,482 viral genomic contigs, which were dereplicated into 111 viral MAGs (vMAGs) of >10 kb in size. As a result of integrating gene expression data with geochemical and metabolite data, we created a conceptual model that uncovered new roles for microorganisms in organic matter decomposition, carbon sequestration, nitrogen mineralization, nitrification, and denitrification. We show how these metabolic pathways, integrated through shared resource pools of ammonium, carbon dioxide, and inorganic nitrogen, could ultimately contribute to carbon dioxide and nitrous oxide fluxes from hyporheic sediments. Further, by linking viral MAGs to these active microbial hosts, we provide some of the first insights into viral modulation of river sediment carbon and nitrogen cycling.

54 ENVIRONMENTAL SCIENCES↗

Assessing individual movement, habitat use, and behavior of non-breeding marine birds in relation to prey availability in the US Atlantic

Resource availability is a key factor driving marine bird movements and distributions, but direct information on prey availability is difficult to obtain at relevant scales. We present novel methods for describing multi-scale trophic associations, combining movement analyses of marine birds with estimates of forage fish surface aggregations from digital aerial survey data and species occupancy from bottom trawl survey data. We analyzed satellite telemetry data from northern gannets Morus bassanus , red-throated loons Gavia stellata , and long-tailed ducks Clangula hyemalis in the US Atlantic during the non-breeding period. Using discrete-time hidden Markov models to distinguish area-restricted (i.e. putative foraging) from transit movements, we examined how environmental factors influence movement, and how forage fish species distributions and surface aggregations influence habitat use by gannets and loons that have greater dietary reliance. Our results suggest that chlorophyll a concentration significantly affected movement behavior across species, highlighting the importance of higher-productivity areas around estuaries during colder months when regional productivity is low. Though variable across species and seasons, spatial cross-correlation analysis revealed that herring species (Family Clupeidae), including Atlantic menhaden Brevoortia tyrannus , may be important resources; it also showed positive spatial correlations with forage fish aggregations. This suggests that prey patch dynamics and factors driving aggregation formation may be as important as species composition. However, spatial patterns were generally low (<0.3), suggesting a mismatch in spatiotemporal resolution, exemplifying the challenges in quantifying trophic relationships in marine systems. Disentangling predator-prey relationships is critical to understanding the mechanisms driving marine bird behavior in rapidly changing marine systems.

Environmental Sciences & Ecology↗

Biomimetic actuators using electroactive polymers (EAP) as artificial muscles

Evolution has resolved many of nature's challenges leading to lasting solutions with maximal performance and effective use of resources. Nature's inventions have always inspired human achievements leading to effective materials, structures, tools, mechanisms, processes, algorithms, methods, systems and many other benefits. The field of mimicking nature is known as Biomimetics and one of its topics includes electroactive polymers that gain the moniker artificial muscles. Integrating EAP with embedded sensors, self-repair and many other capabilities that are used in composite materials can add greatly to the capability of smart biomimetic systems. Such development would enable fascinating possibilities potentially turning science fiction ideas into engineering reality.

Electroactive Polymers (EAP)↗

Action Effectiveness Monitoring and Research of Dredged Material Placement at Woodland Islands (Final Report)

Benthic invertebrates play critical ecosystem roles including the breakdown of organic matter, sediment mixing, and nutrient cycling. In the lower Columbia River and estuary, benthic invertebrates provide a foraging resource for threatened and endangered juvenile salmon. Driven by the goal to create low velocity, shallow water, and riparian shrub habitats to benefit juvenile salmon, the USACE placed 237,000 CY of dredged material, resulting in the deposition of 13.5 acres of sand on the off-channel margins at Woodland Islands. The Pacific Northwest National Laboratory (PNNL) designed and implemented an action effectiveness research study to understand how dredged material placement at Woodland Islands affected sediment conditions and benthic invertebrate assemblages. A Before-After-Control-Impact, or BACI, study design was used to evaluate the response of environmental conditions and benthic invertebrates to dredged material placement. The design included one impact site and two control sites. Sampling occurred for two years prior to dredged material placement and two years after. Our study found that spatial variation was a significant factor for both environmental and biological response variables which suggests local conditions are important considerations for mechanisms affecting benthic assemblages. We found that off-channel habitats across all locations sampled were producing benthic invertebrates, many of which are common prey items for juvenile salmon and steelhead—e.g., insects, chironomids, crustaceans, and corophium. There was a significant BACI effect (i.e., an effect at the dredged material placement site, relative to conditions at the control sites) for concentration of carbon and ammonium in sediment, but not for phosphorous concentrations or for percent sand. The estimated abundance for the three invertebrate response variables—total abundance, total chironomid abundance, and total corophium abundance—was significantly lower at the impact site after dredged material placement, compared to the control sites. At Woodland Island, the estimated mean abundance for all invertebrates combined decreased 28% after dredged material placement. Estimated mean abundances of chironomid and corophium decreased by 8% and 88%, respectively. While invertebrate abundances were lower after dredged placement, the composition of benthic invertebrates was similar before and after placement suggesting that as the new habitat feature evolves recolonization will likely follow. These findings provide a foundation for understanding potential benefits and consequences of repurposing dredged material for habitat creation in the LCRE.

54 ENVIRONMENTAL SCIENCES↗

A modERN resource: identification of Drosophila transcription factor candidate target genes using RNAi

Transcription factors (TFs) play a key role in development and in cellular responses to the environment by activating or repressing the transcription of target genes in precise spatial and temporal patterns. In order to develop a catalog of target genes of Drosophila melanogaster TFs, the modERN consortium systematically knocked down the expression of TFs using RNAi in whole embryos followed by RNA-seq. We generated data for 45 TFs which have 18 different DNA-binding domains and are expressed in 15 of the 16 organ systems. The range of inactivation of the targeted TFs by RNAi ranged from log2fold change -3.52 to +0.49. The TFs also showed remarkable heterogeneity in the numbers of candidate target genes identified, with some generating thousands of candidates and others only tens. We present detailed analysis from five experiments, including those for three TFs that have been the focus of previous functional studies (ERR, sens, and zfh2) and two previously uncharacterized TFs (sens-2 and CG32006), as well as short vignettes for selected additional experiments to illustrate the utility of this resource. The RNA-seq datasets are available through the ENCODE DCC (http://encodeproject.org) and the Sequence Read Archive (SRA). TF and target gene expression patterns can be found here: https://insitu.fruitfly.org. These studies provide data that facilitate scientific inquiries into the functions of individual TFs in key developmental, metabolic, defensive, and homeostatic regulatory pathways, as well as provide a broader perspective on how individual TFs work together in local networks during embryogenesis.

59 BASIC BIOLOGICAL SCIENCES↗

Worth More Dead than Alive? Quantifying Necromass Persistence for Terrestrial Carbon Storage

The continuous cycle of plant-associated microbial biomass growth, death, and decay provides a consistent supply of necromass-C throughout the rooting zone of the soil profile. These inputs are obviously important for resource allocation and soil quality, but microbial necromass-C may play a critical, but currently unknown, role in mitigating the impacts of climate change through atmospheric decarbonization. Microbial necromass is the largest terrestrial sink of persistent carbon in soils, thus its fate and preservation will have a major impact on global C budgets. Our current understanding of the ecosystem controls on necromass generation, biogeochemical transformation, and stabilization is lacking. The objective of this project is to explore the specific influence of rhizosphere and necromass inputs on soil carbon pools.

54 ENVIRONMENTAL SCIENCES↗

Edaphic controls on genome size and GC content of bacteria in soil microbial communities

Nutrient limitation has been shown to reduce bacterial genome size and influence nucleotide composition; however, much of this work has been conducted in marine systems and the factors which shape soil bacterial genomic traits remain largely unknown. Here, for this work, we determined average genome size, GC content, codon usage, and amino acid content from 398 soil metagenomes across a broad geographic range and used machine-learning to determine the environmental parameters that most strongly explain the distribution of these traits. We found that genomic trait averages were most related to pH, which we suggest is primarily due to the correlation of pH with several environmental parameters, particularly soil carbon content. Low pH soils had higher carbon to nitrogen ratios (C:N) and tended to have communities with lower GC content and larger genomes, potentially a response to increased physiological stress and a requirement for metabolic diversity. Conversely, communities in high pH and low soil C:N had smaller genomes and higher GC content—indicating potential resource driven selection against AT base pairs, which have a higher C:N than GC base pairs. Similarly, we found that nutrient conservation also applied to amino acid stoichiometry, where bacteria in soils with low C:N ratios tended to code for amino acids with lower C:N. Together, these relationships point towards fundamental mechanisms that underpin genome size, and nucleotide and amino acid selection in soil bacteria.

54 ENVIRONMENTAL SCIENCES↗

The Evolution of Medical Countermeasures for Ebola Virus Disease: Lessons Learned and Next Steps

The Ebola virus disease outbreak that occurred in Western Africa from 2013–2016, and subsequent smaller but increasingly frequent outbreaks of Ebola virus disease in recent years, spurred an unprecedented effort to develop and deploy effective vaccines, therapeutics, and diagnostics. This effort led to the U.S. regulatory approval of a diagnostic test, two vaccines, and two therapeutics for Ebola virus disease indications. Moreover, the establishment of fieldable diagnostic tests improved the speed with which patients can be diagnosed and public health resources mobilized. The United States government has played and continues to play a key role in funding and coordinating these medical countermeasure efforts. Here, we describe the coordinated U.S. government response to develop medical countermeasures for Ebola virus disease and we identify lessons learned that may improve future efforts to develop and deploy effective countermeasures against other filoviruses, such as Sudan virus and Marburg virus.

59 BASIC BIOLOGICAL SCIENCES↗