Uncovering Hidden Nutrient Dynamics in Algal-Bacterial Consortia: Nanoscale Stable Isotope Probing in the Phycosphere
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Scale-dependent enhancement of productivity and stability in xenic Nannochloropsis cultures
Although bacterial amendments can enhance algal productivity and stability, the development of algal-bacteria consortia for commercial-scale utilization is limited. Here, for this work, we used an established high-throughput approach to generate algal-bacteria consortia, and tested consortia performance at spatial scales from microplates to 320 L raceway ponds. We used both lab and field-reared strains of Nannochloropsis oceanica to build consortia. In some experiments, we imposed environmental perturbations to test the ability of bacteria to enhance algal culture stability. In repeated assays at the scale of well plates, flasks, and bioreactors, strong effects of bacterial amendments on N. oceanica were observed. These effects were most dramatic when cultures experienced stressors such as temperature perturbations or removal of CO 2 augmentation. Isolates that were advanced for field testing included species in the genera Algoriphagus, Oceanicaulis, and Marinobacter. When consortia were generated in the field, positive effects of bacterial amendments were not observed. The amended bacteria were outcompeted, and bacterial community composition across treatments converged after the first grow out. These results highlight the complexity of using consortia in open systems, where interactions between the existing bacterial community, inoculated bacteria, and changing environmental conditions are layered upon other differences in scale and cultivation regimes. Moreover, functionally redundant bacteria are likely present in the field. Following this work, we hypothesize that tight interactions (e.g., obligate relationships between partners) will scale more predictably to outdoor systems. We suggest relying on true synthetic ecological approaches in which the relationships between bacteria and algae partners are well understood, or synthetic ecological approaches coupled with high throughput approaches to design and test consortia. We also recommend future work to examine the effect of algae-bacteria inoculation ratios on productivity and stability, track dynamics of partners through time, and manage ponds to retain beneficial symbioses.
59 BASIC BIOLOGICAL SCIENCES↗
Persistence of bacterial-mediated anti-rotifer protection in preliminary outdoor cultivation trial for Microchloropsis salina
Outdoor algal cultivation systems are susceptible to a wide variety of deleterious species. In previously published studies, we observed protection using microbial consortia at laboratory scale cultures; Microchloropsis salina in the presence of microbial consortia were protected from grazing from the marine rotifer, Brachionus plicatilis. Our objective for the present work was to determine if this protection conferred by microbial consortia in controlled laboratory experiments would persist in an open, outdoor multi-liter cultivation system. We found that algal protection did persist as evidenced by the presence of fewer motile rotifers and decreased rotifer-associated egg counts for the consortia-treated outdoor cultures. Due to the low temperature and light conditions that reduced growth of the algae outdoors, we performed an indoor laboratory assay which also confirmed the persistence of algal protection. Lastly, the lower numbers of motile rotifers and fewer rotifer-associated eggs in the consortia-treated algal cultures suggests a possible protective mechanism by the consortia through interfering with the rotifer lifecycle or reproduction. Finally, these initial results support the possibility that low cost, prophylactic treatments with microbial consortia can protect algae from deleterious species in outdoor cultivation systems.
59 BASIC BIOLOGICAL SCIENCES↗
Predicting partner fitness based on spatial structuring in a light-driven microbial community
Microbial communities have vital roles in systems essential to human health and agriculture, such as gut and soil microbiomes, and there is growing interest in engineering designer consortia for applications in biotechnology ( e . g ., personalized probiotics, bioproduction of high-value products, biosensing). The capacity to monitor and model metabolite exchange in dynamic microbial consortia can provide foundational information important to understand the community level behaviors that emerge, a requirement for building novel consortia. Where experimental approaches for monitoring metabolic exchange are technologically challenging, computational tools can enable greater access to the fate of both chemicals and microbes within a consortium. In this study, we developed an in-silico model of a synthetic microbial consortia of sucrose-secreting Synechococcus elongatus PCC 7942 and Escherichia coli W. Our model was built on the NUFEB framework for Individual-based Modeling (IbM) and optimized for biological accuracy using experimental data. We showed that the relative level of sucrose secretion regulates not only the steady-state support for heterotrophic biomass, but also the temporal dynamics of consortia growth. In order to determine the importance of spatial organization within the consortium, we fit a regression model to spatial data and used it to accurately predict colony fitness. We found that some of the critical parameters for fitness prediction were inter-colony distance, initial biomass, induction level, and distance from the center of the simulation volume. We anticipate that the synergy between experimental and computational approaches will improve our ability to design consortia with novel function.
59 BASIC BIOLOGICAL SCIENCES↗
National Directory of NASA Space Grant Contacts
Congress enacted the National Space Grant College and Fellowship Program (also known as Space Grant). NASA's Space Grant Program funds education, research, and public service programs in all 50 States, the District of Columbia, and the Commonwealth of Puerto Rico through 52 university-based Space Grant consortia. These consortia form a network of colleges and universities, industry partners, State and local Government agencies, other Federal agencies, museum and science centers, and nonprofit organizations, all with interests in aerospace education, research, and training. Space Grant programs emphasize the diversity of human resources, the participation of students in research, and the communication of the benefits of science and technology to the general public. Each year approximately one-third of the NASA Space Grant funds support scholarships and fellowships for United States students at the undergraduate and graduate levels. Typically, at least 20 percent of these awards go to students from underrepresented groups, and at least 40 percent go to women. Most Space Grant student awards include a mentored research experience with university faculty or NASA scientists or engineers. Space Grant consortia also fund curriculum enhancement and faculty development programs. Consortia members administer precollege and public service education programs in their States. The 52 consortia typically leverage NASA funds with matching contributions from State, local, and other university sources, which more than double the NASA funding. For more information, consult the Space Grant Web site at http://education.nasa.gov/spacegrant/
Source record↗
Versatile microbial communities rapidly assimilate ammonium hydroxide-treated plastic waste
Abstract Waste plastic presently accumulates in landfills or the environment. While natural microbial metabolisms can degrade plastic polymers, biodegradation of plastic is very slow. This study demonstrates that chemical deconstruction of polyethylene terephthalate (PET) with ammonium hydroxide can replace the rate limiting step (depolymerization) and by producing plastic-derived terephthalic acid and terephthalic acid monoamide. The deconstructed PET (DCPET) is neutralized with phosphoric acid prior to bioprocessing, resulting in a product containing biologically accessible nitrogen and phosphorus from the process reactants. Three microbial consortia obtained from compost and sediment degraded DCPET in ultrapure water and scavenged river water without addition of nutrients. No statistically significant difference was observed in growth rate compared to communities grown on DCPET in minimal culture medium. The consortia were dominated by Rhodococcus spp., Hydrogenophaga spp., and many lower abundance genera. All taxa were related to species known to degrade aromatic compounds. Microbial consortia are known to confer flexibility in processing diverse substrates. To highlight this, we also demonstrate that two microbial consortia can grow on similarly deconstructed polyesters, polyamides, and polyurethanes in water instead of medium. Our findings suggest that microbial communities may enable flexible bioprocessing of mixed plastic wastes when coupled with chemical deconstruction.
59 BASIC BIOLOGICAL SCIENCES↗
Species-specific ribosomal RNA-FISH identifies interspecies cellular-material exchange, active-cell population dynamics and cellular localization of translation machinery in clostridial cultures and co-cultures
ABSTRACT The development of synthetic microbial consortia in recent years has revealed that complex interspecies interactions, notably the exchange of cytoplasmic material, exist even among organisms that originate from different ecological niches. Although morphogenetic characteristics, viable RNA and protein dyes, and fluorescent reporter proteins have played an essential role in exploring such interactions, we hypothesized that ribosomal RNA-fluorescence in situ hybridization (rRNA-FISH) could be adapted and applied to further investigate interactions in synthetic or semisynthetic consortia. Despite its maturity, several challenges exist in using rRNA-FISH as a tool to quantify individual species population dynamics and interspecies interactions using high-throughput instrumentation such as flow cytometry. In this work, we resolve such challenges and apply rRNA-FISH to double and triple co-cultures of Clostridium acetobutylicum, Clostridium ljungdahlii, and Clostridium kluyveri . In pursuing our goal to capture each organism’s population dynamics, we demonstrate dynamic rRNA, and thus ribosome, exchange between the three species leading to the formation of hybrid cells. We also characterize the localization patterns of the translation machinery in the three species, identifying distinct, dynamic localization patterns among them. Our data also support the use of rRNA-FISH to assess the culture’s health and expansion potential, and, here again, our data find surprising differences among the three species examined. Taken together, our study argues for rRNA-FISH as a valuable and accessible tool for quantitative exploration of interspecies interactions, especially in organisms which cannot be genetically engineered or in consortia where selective pressures to maintain recombinant species cannot be used. IMPORTANCE Though dyes and fluorescent reporter proteins have played an essential role in identifying microbial species in co-cultures, we hypothesized that ribosomal RNA-fluorescence in situ hybridization (rRNA-FISH) could be adapted and applied to quantitatively probe complex interactions between organisms in synthetic consortia. Despite its maturity, several challenges existed before rRNA-FISH could be used to study Clostridium co-cultures of interest. First, species-specific probes for Clostridium acetobutylicum and Clostridium ljungdahlii had not been developed. Second, “state-of-the-art” labeling protocols were tedious and often resulted in sample loss. Third, it was unclear if FISH was compatible with existing fluorescent reporter proteins. We resolved these key challenges and applied the technique to co-cultures of C. acetobutylicum , C. ljungdahlii , and Clostridium kluyveri . We demonstrate that rRNA-FISH is capable of identifying rRNA/ribosome exchange between the three organisms and characterized rRNA localization patterns in each. In combination with flow cytometry, rRNA-FISH can capture sub-population dynamics in co-cultures.
Hill, John D.↗
Changes in environmental and engineered conditions alter the plasma membrane lipidome of fractured shale bacteria
ABSTRACT Microorganisms that persist in fractured shale reservoirs cause several problems including secreting foul gases and forming biofilms. Current biocontrol measures often fail due to limited knowledge of their in situ activities. The plasma membrane protects the cell, mediates many of its critical functions, and responds to intracellular cues and ecological perturbations through physicochemical modifications. As such, it provides valuable insight into the physiological adaptation of microorganisms in disturbed environmental systems. Here, we (i) demonstrate how changes in salinity and hydraulic retention time (HRT) influence the plasma membrane intact polar lipid (IPL) chemistry of model bacterium, Halanaerobium congolense WG10, and mixed microbial consortia enriched from shale-produced fluids and (ii) elucidate adjustments in membrane IPL chemistry during biofilm growth relative to planktonic cells. We incubated H. congolense WG10 in chemostats under three salinities (7%, 13%, and 20% NaCl), operated under three HRTs (19.2, 24, and 48 h), and in drip flow biofilm reactors under the same salinity gradients. Also, mixed microbial consortia in produced fluids were enriched in triplicate chemostat vessels under three HRTs (19.2, 24, and 72 h) and biofilm reactors. Lipids were analyzed by ultra high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Our results show that phosphatidylglycerols, cardiolipins, and phosphatidylethanolamines were predominantly enriched in planktonic H. congolense WG10 cells grown at hypersalinity (20%) compared to optimum (13%). In addition, several zwitterionic phosphatidylcholines and phosphatidylethanolamines were higher in abundance during biofilm growth. These observations suggest that microbial adaptation and biofilm formation in fractured shale are enabled by strategic plasma membrane IPL chemistry adjustments. IMPORTANCE Microorganisms inadvertently introduced into the shale reservoir during fracturing face multiple stressors including brine-level salinities and starvation. However, some anaerobic halotolerant bacteria adapt and persist for long periods of time. They produce hydrogen sulfide, which sours the reservoir and corrodes engineering infrastructure. In addition, they form biofilms on rock matrices, which decrease shale permeability and clog fracture networks. These reduce well productivity and increase extraction costs. Under stress, microbes remodel their plasma membrane to optimize its roles in protection and mediating cellular processes such as signaling, transport, and energy metabolism. Hence, by observing changes in the membrane lipidome of model shale bacteria, Halanaerobium congolense WG10, and mixed consortia enriched from produced fluids under varying subsurface conditions and growth modes, we provide insight that advances our knowledge of the fractured shale biosystem. We also offer data-driven recommendations for improving biocontrol efficacy and the efficiency of energy recovery from unconventional formations.
03 NATURAL GAS↗
Commercial investigation results for the generic bioprocessing apparatus flown on United States Microgravity Laboratory-1
The Generic Bioprocessing Apparatus (BPA) payload was developed by BioServe to support the commercial flight development needs of our specialized consortia comprised of business, academic, and government entities. The consortia have commitments to explore commercial opportunities in bioprocessing, biomedical models, and closed agricultural systems. In addition, some members of BioServe have interests in the development and/or qualification of enabling flight hardware used in life sciences space flight testing. Some business and academic entities have interests in more than one of these consortia. To aid in payload development, flight, and analysis, each consortium member contributes resources ranging from proprietary expertise and materials, to hardware and cash. Professionals from business, academia, and government often interact with each other via graduate research assistants who do much of the 'hands-on' payload preparation and subsequent data analyses. The GBA supported research, testing, and development activities for each different BioServe consortium. It produced an environment in which professionals from diverse backgrounds came together with a single focus. And, it provided a truly novel learning environment for a youthful new cadre of space professionals committed to the exploration of commercial opportunities presented by space. Since the GBA supported a large number of different experiments, this paper briefly describes the payload characteristics and the essential operations of the payload. A summary of the experiments is presented. Finally, a few of the experiments are described in detail highlighting some novel effects of space flight on life science systems. Portions of the reported work have or will appear in appropriate archival journals as cited in the bibliography. In several instances, data collected from USML-1 have been supplemented with related data collected on more recent STS missions.
Stodieck, Louis S.↗
ESMD Space Grant Faculty Report
The strength of the Exploration Systems Mission Directorate ESMD Faculty Project lies in its ability to meet National Aeronautics Space Administration NASA's Strategic Educational Outcome 1 by developing a sustainable and long-term integration of student involvement at academic institutions with all NASA Centers. This outcome is achieved by a three-fold approach: 1) by collecting Senior Design projects pertaining to Constellation work performed at each of the ten NASA Centers, 2) by engaging students at Minority Serving Institutions in the art of systems engineering and systems design of technologies required for space exploration, and 3) by identifying potential internships at each Center relative to exploration that provide students who are supported by their institutional Space Grant to engage in on-going mission-level and explorative systems designs. The objectives of the ESMD Faculty Project are to: 1. Aid the Centers (both Education Offices and associated technical organizations) in providing relevant opportunities for the ESMD Space Grant Program to support student and faculty in Senior Design projects 2. Enable better matches between the ESMD work required and what the Space Grant Consortia can do to effectively contribute to NASA programs 3. Provide the Space Grant Consortia an opportunity to strengthen relations with the NASA Centers 4. Develop better collective understanding of the U.S. Space Exploration Policy by the Center, Space Grant, faculty, Education Office, and students 5. Enable Space Grant institution faculty to better prepare their students to meet current and future NASA needs 6. Enable the Center Education Offices to strengthen their ties to their technical organizations and Space Grant Consortia 7. Aid KSC in gaining a greater and more detailed understanding of each of the Center activities Senior Design projects are intended to stimulate undergraduate students on current NASA activities related to lunar, Mars, and other planetary missions and to bring out innovative and novel ideas that can be used to complement those currently under development at respective NASA Centers. Additionally, such academic involvement would better the prospects for graduating seniors to pursue graduate studies and to seek careers in the space industry with a strong sense for systems engineering and understanding of design concepts. Internships, on the other hand, are intended to provide hands-on experience to students by engaging them in diverse state-of-the-art technology development, prototype bread-boarding, computer modeling and simulations, hardware and software testing, and other activities that provide students a strong perspective of NASA's vision and mission in enhancing the knowledge of Earth and space planetary sciences. Ten faculty members, each from a Space Grant Consortium-affiliated university, worked at ten NASA Centers for five weeks between June 2 and July 3, 2008. The project objectives listed above were achieved. In addition to collecting data on Senior Design ideas and identifying possible internships that would benefit NASA/ESMD, the faculty fellows promoted and collected data when required for other ESMD-funded programs and helped the Center's Education Office, as,needed. 4
Guo, Jiang↗
Worldwide Weather Radar Imagery May Allow Substantial Increase in Meteorite Fall Recovery
Weather radar imagery is a valuable new technique for the rapid recovery of meteorite falls, to include falls which would not otherwise be recovered (e.g. Battle Mountain). Weather radar imagery reveals about one new meteorite fall per year (18 falls since 1998), using weather radars in the United States alone. However, an additional ~75 other nations operate weather radar networks according to the UN World Meteorological Organization (WMO). If the imagery of those radars were analyzed, the current rate of meteorite falls could be improved considerably, to as much as ~3.6 times the current recovery rate based on comparison of total radar areal coverage. Recently, the addition of weather radar imagery, seismometry and internet-based aggregation of eyewitness reports has improved the speed and accuracy of fresh meteorite fall recovery [e.g. 1,2]. This was demonstrated recently with the radar-enabled recovery of the Sutter's Mill fall [3]. Arguably, the meteorites recovered via these methods are of special scientific value as they are relatively unweathered, fresh falls. To illustrate this, a recent SAO/NASA ADS search using the keyword "meteorite" shows that all 50 of the top search results included at least one named meteorite recovered from a meteorite fall. This is true even though only ~1260 named meteorite falls are recorded among the >49,000 individual falls recorded in the Meteoritical Society online database. The US NEXRAD system used thus far to locate meteorite falls covers most of the United States' surface area. Using a WMO map of the world's weather radars, we estimate that the total coverage of the other ~75 national weather radar networks equals about 3.6x NEXRAD's coverage area. There are two findings to draw from this calculation: 1) For the past 16 years during which 18 falls are seen in US radar data, there should be an additional ~65 meteorite falls recorded in worldwide radar imagery. Also: 2) if all of the world's radar data could be analyzed, the rate of recovery of fresh meteorite falls can increase by as much as ~3.6x the current rate. The authors' experience to date indicates that the most effective course of action would be to have local meteorite research groups (outside of the US) form research consortia and develop a working relationship with their nation's weather bureau for access to data. These research consortia could utilize the same, proven methods used for US NEXRAD imagery, internet eyewitness report aggregation, seismometry analysis, etc. to locate meteorite falls. The consortia could then recover and analyze meteorite falls and enrich their own research efforts. It would be beneficial to conduct a global program to coordinate the development of methods and data tools, as well as to coordinate meteorite sample sharing and research. Perhaps an institution such as the Meteoritical Society could lead such an effort.
Fries, Marc↗
The phycosphere and its role in algal biofuel production
Oleaginous microalgae have become a focus for large-scale biofuel production due to their ability to accumulate large quantities of lipids. However, production is currently limited by cost and predation. At present, algal biofuel cultivation is optimized through starvation, supplementing media with nutrients, or genetic engineering; these methods can often be costly with little to no increase in lipid production or the culture’s defense. Investigating the phycosphere of algal-bacterial interactions may overcome these current barriers to large-scale production. The phycosphere of algal-bacterial interactions have formed over millions of years through mutualistic and symbiotic relationships and can provide a more direct source of nutrients compared to adding the nutrients in bulk. The most promising of these interactions include the production of phytohormones and quorum signaling compounds that alter the behaviors of the consortia. Phytohormones can improve algal growth rates, lipid production, and stress resistance. Quorum signaling could create consortia capable of warding off invaders—such as rotifers—while self-regulating and altering behavior based on population density. Mechanisms within the algal phycosphere present many opportunities for the development of novel engineering strategies to further improve algal lipid production and operational costs. This review outlines previous preliminary phycosphere research as well as posing possible opportunities to be pursued in future biofuel production.
09 BIOMASS FUELS↗
Spatiotemporal Metabolic Network Models Reveal Complex Autotroph-Heterotroph Biofilm Interactions Governed by Photon Incidences
Autotroph-heterotroph interactions are ubiquitous in natural environment and play a key role in controlling various essential ecosystem functions, such as production and utilization of organic matter, cycling of nitrogen, sulfur, and other chemical elements. Understanding how these biofilm metabolic interactions are constrained in space and time remains challenging because fully predictive models designed for this purpose are currently limited. Toward filling this gap, here we developed community metabolic network models for two autotroph-heterotroph biofilm consortia (termed UCC-A and UCC-O), which share a suite of common heterotrophic members but have a single distinct photoautotrophic cyanobacterium (Phormidesmis priestleyi str. ANA and Phormidium sp. OSCR) that provides organic carbon and nitrogen sources to support the growth of heterotrophic partners. After determining model parameters by data fitting using the spatiotemporal distributions of microbial abundances, we comparatively analyzed the resulting biofilm models to examine any fundamental differences in microbial interactions between the two consortia under the variation of key environmental variables: CO2 and photon levels. The UCC-A model predicted generally expected responses, i.e., the autotroph population increased in response to elevated levels of CO2 and photon, followed by increase in the heterotroph population. In contrast, the UCC-O model showed somewhat complicated dynamics, e.g., higher photon incidence rates resulted in the increase in autotroph population but decrease in heterotroph population due to the lowered provision of glucose from the autotroph. A further analysis showed that species coexistence was governed by the photon incidences rather than the carbon availability for UCC-O, which was the opposite for UCC-A.
Phalak, Poonam↗
Vitamin interdependencies predicted by metagenomics-informed network analyses and validated in microbial community microcosms
Abstract Metagenomic or metabarcoding data are often used to predict microbial interactions in complex communities, but these predictions are rarely explored experimentally. Here, we use an organism abundance correlation network to investigate factors that control community organization in mine tailings-derived laboratory microbial consortia grown under dozens of conditions. The network is overlaid with metagenomic information about functional capacities to generate testable hypotheses. We develop a metric to predict the importance of each node within its local network environments relative to correlated vitamin auxotrophs, and predict that a Variovorax species is a hub as an important source of thiamine. Quantification of thiamine during the growth of Variovorax in minimal media show high levels of thiamine production, up to 100 mg/L. A few of the correlated thiamine auxotrophs are predicted to produce pantothenate, which we show is required for growth of Variovorax , supporting that a subset of vitamin-dependent interactions are mutualistic. A Cryptococcus yeast produces the B-vitamin pantothenate, and co-culturing with Variovorax leads to a 90-130-fold fitness increase for both organisms. Our study demonstrates the predictive power of metagenome-informed, microbial consortia-based network analyses for identifying microbial interactions that underpin the structure and functioning of microbial communities.
59 BASIC BIOLOGICAL SCIENCES↗
Developing a Process for Collaboration-Based Siting of a Federal Consolidated Interim Storage Facility in the United States: Learning from Communities Living with Legacy Waste
In June of 2023, the U.S. Department of Energy (DOE), Office of Nuclear Energy (NE) announced the selection of its Collaboration-Based Siting (CBS) Consortia, a group of 12 awardees, including the Consortium for Risk Evaluation with Stakeholder Participation (CRESP) (led by Vanderbilt University) to assist DOE-NE with the development of its process for siting a federal consolidated interim storage facility (FCISF) for spent nuclear fuel (SNF) storage. At this time, DOE NE is not soliciting interested host communities, rather the CBS Consortia are tasked with in-depth engagement, mutual learning, and capacity building to provide DOE NE with feedback on the CBS process. CRESP’s objective is to engage communities in two regions (the Pacific Northwest and the Southeast) with sites currently storing defense- and research-related SNF to foster learning concerning the best and worst practices in community participation in risk-informed decision making. This includes learning from existing structures for public input in radioactive waste management decision making [e.g. citizen advisory boards (CABs)] and other local parties about how to build and sustain trust among the parties. CRESP has been working to engage stakeholders and Tribes surrounding two DOE sites historically differing in receptiveness to engaging with DOE and trusting in DOE to accomplish its missions. CRESP’s approach to date has consisted of (1) engaging voluntarily members and former members of the DOE Office of Environmental Management’s CABs to develop a mutual understanding of their perspectives, values, and experiences related to risk and participatory decision making; (2) engaging members of those communities that would likely be part of any radioactive waste management discussions and who may provide valuable feedback for the development of the CBS process; and in the longer term, (3) engaging communities to foster knowledge sharing on understanding and definitions of risk and how risk is factored into community decision making. Our emphasis is to identify opportunities for improving risk communication frameworks, strategies, and decision making. The selection of a future FCISF site is likely to result in the creation of a structure similar to a CAB composed of members of the local community. We anticipate that these insights can help DOE NE learn from existing participatory risk communication structures in place at sites storing defenseor research-related SNF to understand best practices for fostering enduring and participatory relationships with future CABs. Within this paper, we (1) describe CRESP’s overall approach to assisting DOE NE with maturing the CBS process; (2) present a summary of preliminary phase 1 project results, including the development of a body of knowledge (describing available resources to support community engagement, risk communica tion, and participatory decision making) and community ecosystem information (leveraging demographic, social, economic, and environmental attribute mapping and advanced sentiment analysis of social media data); and (3) based on these results, provide observations for future research opportunities to support the development of CBS processes for radioactive waste management facilities, generally.
collaboration-based siting↗
Microbial sensor variation across biogeochemical conditions in the terrestrial deep subsurface
ABSTRACT Microbes can be found in abundance many kilometers underground. While microbial metabolic capabilities have been examined across different geochemical settings, it remains unclear how changes in subsurface niches affect microbial needs to sense and respond to their environment. To address this question, we examined how microbial extracellular sensor systems vary with environmental conditions across metagenomes at different Deep Mine Microbial Observatory (DeMMO) subsurface sites. Because two-component systems (TCSs) directly sense extracellular conditions and convert this information into intracellular biochemical responses, we expected that this sensor family would vary across isolated oligotrophic subterranean environments that differ in abiotic and biotic conditions. TCSs were found at all six subsurface sites, the service water control, and the surface site, with an average of 0.88 sensor histidine kinases (HKs) per 100 genes across all sites. Abundance was greater in subsurface fracture fluids compared with surface-derived fluids, and candidate phyla radiation (CPR) bacteria presented the lowest HK frequencies. Measures of microbial diversity, such as the Shannon diversity index, revealed that HK abundance is inversely correlated with microbial diversity ( r 2 = 0.81). Among the geochemical parameters measured, HK frequency correlated most strongly with variance in dissolved organic carbon ( r 2 = 0.82). Taken together, these results implicate the abiotic and biotic properties of an ecological niche as drivers of sensor needs, and they suggest that microbes in environments with large fluctuations in organic nutrients (e.g., lacustrine, terrestrial, and coastal ecosystems) may require greater TCS diversity than ecosystems with low nutrients (e.g., open ocean). IMPORTANCE The ability to detect extracellular environmental conditions is a fundamental property of all life forms. Because microbial two-component sensor systems convert information about extracellular conditions into biochemical information that controls their behaviors, we evaluated how two-component sensor systems evolved within the deep Earth across multiple sites where abiotic and biotic properties vary. We show that these sensor systems remain abundant in microbial consortia at all subterranean sampling sites and observe correlations between sensor system abundances and abiotic (dissolved organic carbon variation) and biotic (consortia diversity) properties. These results suggest that multiple environmental properties may drive sensor protein evolution and highlight the need for further studies of metagenomic and geochemical data in parallel to understand the drivers of microbial sensor evolution.
response regulator↗
Soil microbiome interventions for carbon sequestration and climate mitigation
Mitigating climate change in soil ecosystems involves complex plant and microbial processes regulating carbon pools and flows. Here, we advocate for the use of soil microbiome interventions to help increase soil carbon stocks and curb greenhouse gas emissions from managed soils. Direct interventions include the introduction of microbial strains, consortia, phage, and soil transplants, whereas indirect interventions include managing soil conditions or additives to modulate community composition or its activities. Approaches to increase soil carbon stocks using microbially catalyzed processes include increasing carbon inputs from plants, promoting soil organic matter (SOM) formation, and reducing SOM turnover and production of diverse greenhouse gases. Marginal or degraded soils may provide the greatest opportunities for enhancing global soil carbon stocks. Among the many knowledge gaps in this field, crucial gaps include the processes influencing the transformation of plant-derived soil carbon inputs into SOM and the identity of the microbes and microbial activities impacting this transformation. As a critical step forward, we encourage broadening the current widespread screening of potentially beneficial soil microorganisms to encompass functions relevant to stimulating soil carbon stocks. Moreover, in developing these interventions, we must consider the potential ecological ramifications and uncertainties, such as incurred by the widespread introduction of homogenous inoculants and consortia, and the need for site-specificity given the extreme variation among soil habitats. Incentivization and implementation at large spatial scales could effectively harness increases in soil carbon stocks, helping to mitigate the impacts of climate change.
54 ENVIRONMENTAL SCIENCES↗
Syntrophic Co-Cultures of Clostridium Organisms to Produce Higher Alcohols & Other C6-C8 Metabolites (Final Report)
The goal of this project was to advance the systems biology understanding and predictive modeling of synthetic & syntrophic Clostridium microbial consortia, focusing on elucidation of metabolic networks and environmental signals in the consortia. The project has direct applicability to lignocellulosic-biomass based production of higher alcohols as advanced biofuels and C6-C8 metabolites, that can be used as chemicals or serve as biofuel precursors. This project studied and optimized three synthetic syntrophic systems. It examined the population dynamics using flow-cytometry, time-lapse microscopy and PCR analysis. 13C-based tracer analyses was used to examine the metabolite exchange between the syntrophic cell populations and the impact of those interactions on the transcriptome of the individual populations. To enhance our analytical and predictive capabilities, genome-scale models (GSMs) for these syntrophies was developed. RNAseq data for these syntrophic coculture systems were acquired to enable a molecular level understanding of the syntrophies aiming to identify the genetic networks of each organism in the co-culture and compare those against the networks of pure cultures.
09 BIOMASS FUELS↗