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At least 523 records · Page 29

Functional capacities of microbial communities to carry out large scale geochemical processes are maintained during ex situ anaerobic incubation

Mechanisms controlling CO 2 and CH 4 production in wetlands are central to understanding carbon cycling and greenhouse gas exchange. However, the volatility of these respiration products complicates quantifying their rates of production in the field. Attempts to circumvent the challenges through closed system incubations, from which gases cannot escape, have been used to investigate bulk in situ geochemistry. Efforts towards mapping mechanistic linkages between geochemistry and microbiology have raised concern regarding sampling and incubation-induced perturbations. Microorganisms are impacted by oxygen exposure, increased temperatures and accumulation of metabolic products during handling, storage, and incubation. We probed the extent of these perturbations, and their influence on incubation results, using high-resolution geochemical and microbial gene-based community profiling of anaerobically incubated material from three wetland habitats across a permafrost peatland. We compared the original field samples to the material anaerobically incubated over 50 days. Bulk geochemistry and phylum-level microbiota in incubations largely reflected field observations, but divergence between field and incubations occurred in both geochemistry and lineage-level microbial composition when examined at closer resolution. Despite the changes in representative lineages over time, inferred metabolic function with regards to carbon cycling largely reproduced field results suggesting functional consistency. Habitat differences among the source materials remained the largest driver of variation in geochemical and microbial differences among the samples in both incubations and field results. While incubations may have limited usefulness for identifying specific mechanisms, they remain a viable tool for probing bulk-scale questions related to anaerobic C cycling, including CO 2 and CH 4 dynamics.

59 BASIC BIOLOGICAL SCIENCES↗

Soil microbial ecology and microbiome-metabolite linkages improve understanding of ecosystem states along terrestrial-aquatic interfaces

These data are from Bandopadhyay et al., "Soil microbial ecology and microbiome-metabolite linkages improve understanding of ecosystem states along terrestrial-aquatic interfaces". This study aims to understand the soil microbial ecology along terrestrial-aquatic interfaces of a freshwater and estuarine region and how it relates to organic matter. We analyzed soil microbial (16S rRNA gene) and organic matter (Fourier-transform ion cyclotron resonance mass spectrometry, FTICR-MS) composition from upland (forested), transition (stressed forest), and wetland positions at three sites in each of the Lake Erie (freshwater) and Chesapeake Bay (estuarine) regions. This dataset includes 16S rRNA gene amplicon data (only processed file types included here) and organic matter composition from FTICR-MS data (raw and processed files included here) from upland (forested), transition (stressed forest), and wetland positions at three sites in each of the Lake Erie and Chesapeake Bay regions. These sites are part of the COMPASS-FME project (https://compass.pnnl.gov/FME/COMPASSFME). File formats and software needed to access files: 16S rRNA gene amplicon data: These files follow the format reported here https://ess-dive.gitbook.io/amplicon-sequencing-reporting-format#updates-in-v1.0.1. As per this format, there are four file types reported: 1. Taxon tables (also called sequence-by-sample or OTU (operational taxonomic unit)/ESV (exact sequence variant) tables) : available in a .txt file format and accessible using TextEdit or MS Excel. 2. Representative sequences (also called consensus sequences) : available in a .fasta format and accessible using TextEdit. 3. Sequencing metadata : available in a MS Excel workbook file format and CSV file format 4. Bioinformatic metadata : available in a MS Excel workbook file format and CSV file format FTICR-MS data: 1. Raw data converted to a processed file with intensities of the peaks in the given samples : available in a MS Excel CSV file format 2. Processed file used in analyses and visualizations (appended as icr_long_) : available in a MS Excel CSV file format 3. Metadata file for ICR features (appended as icr_meta) : available in a MS Excel CSV file format

54 ENVIRONMENTAL SCIENCES↗

Catalytic Hydroprocessing of Single-Cell Oils to Hydrocarbon Fuels : Converting microbial lipids to fuels is a promising approach to replace fossil fuels

Microbial lipids hold great promise as biofuel precursors, and research efforts to convert such lipids to renewable diesel fuels have been increasing in recent years. In contrast to the numerous literature reviews on growing, characterising and extracting lipids from oleaginous microbes, and on converting vegetable oils to hydrocarbon fuels, this review aims to provide insight into aspects that are specific to hydroprocessing microbial lipids. While standard hydrotreating catalysts generally perform well with terrestrial oils, differences in lipid speciation and the presence of co-extracted compounds, such as chlorophyll and sterols, introduce additional complexities into the process for microbial lipids. Lipid cleanup steps can be introduced to produce suitable feedstocks for catalytic upgrading.

09 BIOMASS FUELS↗

Collaborative Research: Natural Organic Matter and Microbial Controls on Mobilization/Immobilization of I and Pu in Soils and Waters Affected by Radionuclide Releases in USA and Japan

In this project, the relationship between natural organic matter (NOM) and two radioactive elements that are relevant to nuclear waste disposal were studied: Plutonium (Pu) and Iodine. The human and environmental risks associated with Pu stem mainly from the very long half-lives of several of its isotopes ( 238 Pu, 88 yr; 239 Pu, 24,100 yr; 240 Pu, 6560 yr) and its radiotoxicity. Understanding Pu biogeochemical behavior in both near-field (>10-11M) and far-field scales (<10-11M) is imperative to the development of approaches for reprocessing Pu, remediation of Pu contamination and accurate assessment of risks posed by disposal practices for Pu-bearing wastes. The environmental mobility of Pu can be affected by redox potential, pH, adsorption, precipitation, complexation, colloid formation, and microbial activity, of which the first characteristic has the most profound influence. Numerous studies have shown high affinity of Pu towards NOM, as well as to mineral phases. NOM is ubiquitous in the environment, e.g., both fulvic and humic acids are able to reduce Pu(V,VI) to Pu(IV) and the redox potential of NOM is positively related to the abundance of phenolic/acidic OH groups. NOM can either facilitate or limit actinide migration, depending on specific biogeochemical conditions including pH, mineral and organic matter characteristics, etc. The other radionuclide of interest is radioiodine ( 129 I). 129I is a major by-product of nuclear fission and of serious concern to the Department of Energy (DOE) as it is among the top risk drivers at existing and potential radiowaste-contaminated sites. The risk of 129 I stems largely from its high bioconcentration factor (90% of the body’s iodine is accumulated in the thyroid), a high inventory at source terms, a very long-half life (16M years), and rapid mobility in the subsurface environment. As a consequence, 129 I has the lowest drinking water standard (1 pCi/L) among all radionuclides in the Federal Register. With a novel and sensitive gas chromatography-mass spectrometry (GC-MS) method developed in our lab, it is possible to quickly and simultaneously determine the distribution of 129 I and stable 127 I forms in environments, as low as 2 pCi/L for 129 I. This method was subsequently validated using accelerator mass spectroscopy, AMS. IO 3 - and organo-I were determined as major species in the groundwater of SRS and the Hanford Site, contrary to thermodynamic predictions that I- should be the dominant species at these sites. Mobility of 129 I was also demonstrated to depend greatly on the I species and its concentration, sediment pH, and redox state, with times to achieve equilibrium taking up to 12 weeks. Along the groundwater pathway in the F-Area of SRS, 129 I- supplied from the seepage basins was transformed to 129 IO 3 - and organo- 129 I with increasing iodine sediment sorption, causing the lower total 127 I and 129 I concentrations along the gradient transect of the waste plume. By contrast, groundwater 129 I concentrations in the wetlands (as high as 1617.3 pCi/L) were greatly elevated with respect to the source term (159.3 pCi/L). While the NOM promoted the uptake of 129 I to the wetland sediment, it also promoted the formation of soluble organic fraction. A small fraction of NOM that is bound to iodine can behave as a mobile organo-I source. Iodide was enzymatically incorporated into NOM, whereas both iodide and iodate were abiotically bound to NOM, under certain conditions. Iodate removal from the mobile aqueous phase can also occur through incorporation into carbonate (e.g., at the Hanford Site, USA). Thus immobilization and re-mobilization of iodine species were influenced by pH, Eh and the presence of NOM and metal oxides, which adds to the complexity of site remediation action. A ground-breaking result was to elucidate the products (i.e. organo-iodine moieties formed via enzymatic and non-enzymatic processes) at the molecular level by nuclear magnetic resonance (NMR) and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS). We found that iodine-NOM interactions may be influenced by NOM hydrophobic aliphatic moieties. From the perspective of ESI-FTICRMS, organo-iodine formulas were ascribed to the groups of unsaturated hydrocarbons, lignins and proteins. Iodate is likely abiotically reduced to reactive iodine species by lignin- and tannin-like compounds or carboxylic-rich alicyclic molecules (CRAM). We also investigated microbial mechanisms in iodine incorporation into NOM. We established that soil bacteria isolated from F-Area of SRS did not accumulate significant amounts of I- (0.2-2%). Intracellular uptake of I- decreases with increasing pH when pH ranged from 4 to 6. In contrast, 44 out of 84 strains isolated from the F-Area of SRS can transform I- to IO 3 - and organo-iodine. In some cases, oxidation was facilitated in the presence of H 2 O 2 . Microbes can also excrete organic acids that enhance I- oxidation by lowering the ambient pH and reacting with H 2 O 2 to form peroxy carboxylic acids. At lower pH values (≤5), H 2 O 2 hydrolysis was the driving force for iodide-oxidation; whereas, at pH ≥ 6, spontaneous decomposition of peroxy carboxylic acids, originating from H 2 O 2 and organic acids were the primary cause of iodide oxidation. Lastly, it was determined that microbial processes involved in Mn (II) are capable of directly oxidizing I- via enzymatic catalysis (i.e., multicopper oxidases), or indirectly through the formation of reactive oxygen species (ROS) and/or biogenic manganese oxides. ROS-mediated oxidation of I- was found to predominate at pH >5, whereas the enzymatic and Mn oxide pathways were more active at pH < 5. Together, this project has resulted in 9 publications in high-impact journals, and the training of 1 Ph.D and 4 undergraduate students.

54 ENVIRONMENTAL SCIENCES↗

The Influence of Microbial Priming Effects on the Hydro-bio-geochemistry of Large River Reservoirs

River-tributary confluences, where diverse organic matter (OM) sources mix, are considered aquatic critical zones for biogeochemical cycling. Here we evaluate dissolved OM composition and bioavailability in the mainstem of the Columbia River and three of its tributaries (Snake, Yakima, and Walla Walla rivers) along a hydrologic gradient in the Columbia River drainage basin using a variety of bulk and molecular level measurements. Field replicates and mixtures representing river-tributary confluences were incubated in the dark for 15 days to investigate the response of the microbial community to varying OM quantity/composition. The Columbia, Snake, and Yakima rivers did not differ in dissolved organic carbon (DOC), fluorescent dissolved OM (fDOM), or Chlorophyll-a (Chl-a) concentrations. However, the Walla Walla River had significantly greater DOC, fDOM, and Chl-a concentrations, indicative of greater contributions from algal DOM. FT-ICR-MS spectra for Walla Walla had significantly more peaks corresponding to amino sugars, carbohydrates and proteins while the Columbia River had more peaks for lignin, unsaturated hydrocarbons, and condensed aromatics. When incubated for 15 days in the dark, total DOC did not decrease for any of the river samples. DOC did decrease, however, in a mix representing the confluence of the Columbia and Walla Walla rivers, suggesting the microbial consortia of the Columbia River were primed by the Walla Walla River OM. OM composition was significantly different for several compound classes (e.g., lignin, protein, and tannin) following the incubations of unmixed river and tributary samples. However, the microbial community in the Walla Walla-Columbia mixture appeared to be indiscriminate of the molecular structure of the DOM as the compound class distribution did not change significantly. This provides preliminary evidence that the heterotrophs in river-tributary critical zones remineralize diverse OM structures.

54 ENVIRONMENTAL SCIENCES↗

DOE Support for the North American meeting of the International Society for Microbial Electrochemistry and Technology

The objective of the North American meeting of the International Society for Microbial Electrochemistry and Technology (NA-ISMET 2021, postponed from 2020 due to COVID-19) was to provide a welcoming space for an interdisciplinary group of researchers, primarily based in North America, to discuss their latest discoveries and innovative ideas on both basic science and applied technology in the field of microbial electrochemistry. After two years of limited travel and research interactions due to COVID-19, an in-person meeting was urgently needed to facilitate conversations and collaborations that help move the field forward. NA-ISMET 2021 was co-organized by Moh El-Naggar from the University of Southern California (USC) and Orianna Bretschger from Aquacycl Inc. The meeting took place on November 17 – 19, 2021 at the Michelson Center for Convergent Biosciences of USC. We hosted a total number of 65 registered participants from across the United States and several international participants. Thanks to the generous support from the Department of Energy, Air Force Office of Scientific Research, Office of Naval Research, the Army Research Office, the ISMET organization, and Gamry Instruments Inc., we were able to waive registration fees for all participants and reduce travel cost for several early-career researchers. The scientific program included 28 talks (16 from early-career researchers) and 24 posters that highlighted recent advances in microbial electrochemistry.

30 DIRECT ENERGY CONVERSION↗

Deciphering exopolysaccharide functional specificity via visualization of chemical motifs that mediate microbial-microenvironment interactions in soil micromodels

Exopolysaccharides (EPS) are carbohydrate-based matrices of microbial biofilms that microbes use to adapt to their surroundings. Microbial EPS also promotes soil aggregate stability and contributes toward soil health by reducing erosion caused by continued land use. The chemical structure of EPS, even within single species biofilms, can vary greatly: from repeating units and branching patterns to the non-carbohydrate decorations. Despite the wealth of knowledge on EPS chemistry, many unresolved questions regarding the biological implications of EPS chemical variations remain. Here, we develop a mass spectrometry imaging toolbox that reveal how EPS chemistry enables microbial adaptation to different microenvironments such as specific moisture, soil-biofilm interfaces, and food source proximity. First, we developed emulated soil micromodels (ESMs), microfluidic channels that simulate the physical properties of soil, for biofilm formation in different microenvironments. Then, in order to map chemical features of EPS in these micromodels, we develop strategies for in-situ releasing of oligosaccharides using specific enzymes. Lastly, we optimized matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging (MSI) to spatially analyze the released compounds in ESMs.

54 ENVIRONMENTAL SCIENCES↗

Multi-scale Simulation, Calibration, and Optimization of Calcium Carbonate Precipitation in Microbial Communities

Ensuring the efficient engineering of microbially induced calcium carbonate precipitation (MICP) is crucial for a variety of environmental and civil engineering applications, such as soil stabilization and carbon sequestration. Addressing this need, we present a comprehensive multi-scale workflow that begins with the isolation of calcium carbonate-producing microbes from soil samples, followed by metagenomic sequencing and metabolic reconstruction. We then characterize microbial growth phenotypes under diverse nutrient conditions, compare observed growth with metabolic model predictions, and apply the Consistent Reproduction of Phenotype (CROP) algorithm to refine these models. Furthermore, we analyze metabolite consumption and production, and develop a consumer-resource model that is calibrated using time-series measurements of growth rates, pH levels, and calcium carbonate precipitation. The primary benefit of our approach lies in its ability to predict and control MICP outcomes, facilitated by a Bayesian methodology that incorporates priors on initial conditions and parameters. This allows us to compute posteriors by integrating experimental data, and to solve a risk optimization problem under uncertainty to identify nutrient conditions that maximize calcium carbonate production. In contrast to non-Bayesian methods, which fail to quantify uncertainty accurately, our approach provides a more reliable pathway to optimizing nutrient conditions, enhancing the likelihood of achieving desired MICP outcomes. This positions our method as a superior alternative in the quest to improve MICP through engineered microbial consortia.

54 ENVIRONMENTAL SCIENCES↗

Geochemical and Microbial Dynamics of Hydrogen in a Methane Storage Reservoir

Hydrogen has been identified as a flexible energy carrier with zero or negative emission across multiple energy systems, and existing natural gas infrastructure could be leveraged if hydrogen gas (H2) was blended with methane (CH4). For example, subsurface methane storage reservoirs could be slightly modified to also store hydrogen if a methane/hydrogen blend were injected. However, the compatibility of methane storage reservoirs to include H2 injection has not been fully demonstrated, and this could lead to geochemical and microbiological reactions that alter the reservoir and stored gas content. It is essential that we understand the impact of H2 gas on the biogeochemistry of subsurface storage reservoirs before deploying large-scale H2-CH4 storage, We collected produced fluid from two separate methane storage reservoirs in the Southwestern US. First, we completed a baseline analysis of the biogeochemistry through qPCR, 16S rRNA sequencing, metagenomic sequencing, and geochemical analysis. Each reservoir was found to have unique geochemical conditions and a unique microbial community structure, with Site 1 having a higher TDS and an abundance of Shewanella and Site 2 having a lower TDS and high abundance of Eubacterium and Acetobacterium. Next, we ran a series of high pressure, high temperature reactors under hydrogen storage conditions with the biological sample from one of the storage reservoirs and a 20% H2-80% CH4 gas blend for up to 7 days. Our results show a decrease of hydrogen by 5% in reactors as early as 1-3 days. Previous hydrogen storage work has linked subsurface microorganisms with methanogenesis hydrogen sulfide production, acid production, and microbial corrosion. Our results show minimal change in the fluid chemistry, with the exception of a decrease in dissolved sulfate concentrations. Taxonomic sequencing demonstrated the presence of microorganisms capable of iron redox, acid generation, and hydrogen sulfide production throughout the reactors, suggesting microbial hydrogen consumption may occur through various metabolic pathways. This work demonstrates that site-specific geochemistry and microbiology may impact the efficiency of hydrogen storage in methane storage reservoirs.

environmental microbiology↗

Fungal Community, Not Substrate Quality, Drives Soil Microbial Function in Northeastern U.S. Temperate Forests

Mycorrhizal fungi can affect soil organic matter cycling through several mechanisms including priming, nutrient competition, and direct enzyme production. Differences in nutrient foraging strategies between ectomycorrhizal (EcM) and arbuscular mycorrhizal (AM) fungi produce divergent belowground dynamics: where EcM can take up organic nitrogen and directly break down soil organic matter (SOM) by producing enzymes, AM fungi are limited to scavenging mineral N. EcM-associated tree species also have leaf litter with relatively higher ratios of carbon to nitrogen (C:N), and belowground saprotrophic communities more dominated by fungi. Consequently, free-living microbes in EcM-dominated soils should experience nitrogen limitation, with subsequent increases in enzyme production and decreased carbon use efficiency (CUE). However, the relative importance of the effects of substrate quality and fungal community composition on enzyme production and CUE are unclear. To assess this distinction, we sampled the organic horizon and 10 cm of the mineral horizon in northern temperate forest soils along a gradient of EcM dominance. We characterized fungal community composition by measuring EcM relative abundances from extracted fungal DNA and the fungal to bacterial (F:B) ratios from phospholipid fatty acid (PLFA) analysis. We assessed soil substrate quality as the soil C:N ratio. Soil microbial functions were measured as potential activities of five hydrolytic and two oxidative enzymes, and microbial CUE. We found that the fungal community, represented by either the F:B ratio, EcM relative abundance, or both, affected CUE and six measured enzyme activities, while the C:N ratio affected only oxidative and chitin-targeting extracellular enzyme activities. Our results highlight the use of EcM relative dominance as a predictor of soil microbial community composition and function independent of substrate quality.

54 ENVIRONMENTAL SCIENCES↗

Nutrient Exposure Alters Microbial Composition, Structure, and Mercury Methylating Activity in Periphyton in a Contaminated Watershed

The conversion of mercury (Hg) to monomethylmercury (MMHg) is a critical area of concern in global Hg cycling. Periphyton biofilms may harbor significant amounts of MMHg but little is known about the Hg-methylating potential of the periphyton microbiome. Therefore, we used high-throughput amplicon sequencing of the 16S rRNA gene, ITS2 region, and Hg methylation gene pair (hgcAB) to characterize the archaea/bacteria, fungi, and Hg-methylating microorganisms in periphyton communities grown in a contaminated watershed in East Tennes(see United States). Furthermore, we examined how nutrient amendments (nitrate and/or phosphate) altered periphyton community structure and function. We found that bacterial/archaeal richness in experimental conditions decreased in summer and increased in autumn relative to control treatments, while fungal diversity generally increased in summer and decreased in autumn relative to control treatments. Interestingly, the Hg-methylating communities were dominated by Proteobacteria followed by Candidatus Atribacteria across both seasons. Surprisingly, Hg methylation potential correlated with numerous bacterial families that do not contain hgcAB, suggesting that the overall microbiome structure of periphyton communities influences rates of Hg transformation within these microbial mats. To further explore these complex community interactions, we performed a microbial network analysis and found that the nitrate-amended treatment resulted in the highest number of hub taxa that also corresponded with enhanced Hg methylation potential. This work provides insight into community interactions within the periphyton microbiome that may contribute to Hg cycling and will inform future research that will focus on establishing mixed microbial consortia to uncover mechanisms driving shifts in Hg cycling within periphyton habitats.

59 BASIC BIOLOGICAL SCIENCES↗

Antibiotic resistance and host immune system-induced metal bactericidal control are key factors for microbial persistence in the developing human preterm infant gut microbiome

The human gut microbiome, which develops and stabilizes during the early stages of infant life, plays an essential role in host health through the production of metabolic resources and the stimulation and training of the immune system. To study colonization and community functional dynamics of the microbiota based on responses to host immune processes during the normal and dysbiotic establishment of the gut, metaproteomics was conducted on 91 fecal samples collected over the first 90 days of life from 17 hospitalized premature infants. Microbial responses to antibiotic administration and host-imposed metal bactericidal control correlated with community assembly and resiliency of microbes in the developing preterm gut. Specifically, proteins related to antibiotic resistance and metal homeostasis mechanisms were predominant in persisting members in the infant gut environment over the first several weeks of life. Overall, this metaproteomics study provides a unique approach to examine the temporal expansion and resilience of microbial colonization, as it allows simultaneous examination of both host and microbial metabolic activities. Understanding the interplay between host and microbes may elucidate the microbiome’s potential immunomodulatory roles relevant to necrotizing enterocolitis and other dysbiotic conditions in preterm infants.

59 BASIC BIOLOGICAL SCIENCES↗

Effects of Cinnamomum camphora coppice planting on soil fertility, microbial community structure and enzyme activity in subtropical China

Cinnamomum camphora ( C. camphora ) is a broad-leaved evergreen tree cultivated in subtropical China. Currently, the use of C. camphora clonal cuttings for coppice management has become popular. However, the effects of C. camphora coppice planting on soil abiotic and biotic variances remained unclear. In this study, we collected soil from three points in the seven-year C. camphora coppice planting land: under the tree canopy (P15), between trees (P50), and abandoned land (Control) to investigate the effects of C. camphora coppice planting on soil fertility, microbial community structure and enzyme activity. The results revealed that C. camphora coppice planting significantly increased soil fertility in the point under the tree canopy (P15) and point between trees (P50), and P15 had more significant effects than P50. Meanwhile, in P15 and P50, soil bacterial, fungal alpha-diversity were improved and microbial community structures were also changed. And the changes of soil organic carbon and total nitrogen promote the transformation of soil bacterial, fungal community structures, respectively. In addition, C. camphora coppice planting significantly ( p < 0.05) increased soil urease (UE), polyphenol oxidase, and peroxidase activities, while significantly decreased soil ACP activity. This study demonstrated that the C. camphora coppice planting could improve soil fertility in subtropical China, which promoted the transformation of soil microbial community from oligotrophs ( K -strategist) to copiotrophs ( r -strategist). Thus, this work can provide a theoretical basis for soil nutrient variation and productive management of C. camphora coppice plantation in subtropical China.

Sun, Luyuan↗

In anaerobic reactors the microbial community structure depends on feed type, with no “keystone” species tied to COD removal

Two-stage anaerobic digestion (AD) systems provide treatment for high strength wastewater with high stability and performance. Encapsulation technology can intensify AD to facilitate the separation of the solids retention time from the hydraulic retention time (HRT), offering lower HRTs, smaller reactors, and high effluent quality. To support successful deployment, however, the encapsulated community must contain all the needed microorganisms for successful treatment and be flexible enough to treat a variety of wastewaters. Here, a two-stage system was investigated in which microbial cultures were enriched on various high-strength wastewaters in suspended flow-through systems to determine how feed type influenced performance and microbial community structure. The hypothesis was that specific genera, or so-called “keystone species” would positively correlate to organic carbon degradation for a given feed, enabling construction of a well-functioning community for encapsulation. Results showed that the number of total bacteria (as 16S rRNA gene copies) did not correlate to soluble chemical oxygen demand (sCOD) removal, indicating that the community structure and/or members were important for good performance. Results also showed that feed type strongly influenced carbon removal and microbial community structure for 1st-stage fermenting communities, but not 2nd-stage methanogenic communities. In this study, the “core” community members were defined as organisms common to all of either the 1st- or 2nd-stage reactors irrespective of the feed they received and were present in at least 50% of the samples throughout the entire experiment. “Unique” community members were specific to a single feed, and hence, only present in either the 1st- or 2nd-stage reactors receiving that feed. In both 1st- and 2nd-stage communities, only one core genera and no unique genera were positively and significantly correlated to sCOD removal. Verification experiments performed with encapsulated communities showed that organisms identified in flow-through system and correlated with carbon degradation, though not significantly, seemed to be important for performance. Our results suggest that one cannot construct a community containing specific populations in lieu of enrichment. Nevertheless, a single diverse encapsulated anaerobic community should provide good (>80%) carbon removal when fed a variety of influents, if time is provided for enrichment after deployment.

54 ENVIRONMENTAL SCIENCES↗

Effect of Temperature and pH on Microbial Communities Fermenting a Dairy Coproduct Mixture

Organic-rich industrial residues can serve as renewable feedstocks for the generation of useful products by microbial fermentation. We investigated fermenting communities enriched in a mixture of ultra-filtered milk permeate (UFMP) and acid whey from cottage cheese (CAW), two dairy coproducts rich in lactose. To evaluate how operational pH and temperature affect microbial communities and fermentation products, we operated 12 bioreactors for 140 days, each fed a 1:1 mixture of UFMP and CAW at either 35 °C or 50 °C and at either a pH of 4.8 or 5.5. The bioreactors operated at a pH of 4.8 resulted in the incomplete conversion of lactose, while those operated at a pH of 5.5 consistently fermented lactose, primarily into lactic, acetic, and hexanoic acids. The metagenomic analyses revealed that microbial communities obtained at a pH of 5.5 were dominated by lactic acid-producing organisms. Additionally, an inverse relationship was found between the abundance of chain elongating organisms and lactic acid accumulation, with 50 °C reducing the abundance of these organisms and enhancing lactic acid yields. We conclude that the pH and temperature are important determinants of the fermentation of dairy coproducts with a pH of 5.5 and 50 °C yielding the most promising results for lactic acid production. Additional research is required to better understand the factors affecting functional consistency of the process.

Biotechnology & Applied Microbiology↗

One Health Approach to Tackle Microbial Contamination on Poultries—A Systematic Review

This study reports the search of available data published regarding microbial occupational exposure assessment in poultries, following the PRISMA methodology. Air collection through filtration was the most frequently used. The most commonly used passive sampling method was material collection such as dust, cages, soils, sediment, and wastewater. Regarding assays applied, the majority of studies comprised culture-based methods, but molecular tools were also frequently used. Screening for antimicrobial susceptibility was performed only for bacteria; cytotoxicity, virological and serological assays were also performed. Most of the selected studies focused on bacteria, although fungi, endotoxins, and β-glucans were also assessed. The only study concerning fungi and mycotoxins reported the carcinogenic mycotoxin AFB1. This study gives a comprehensive overview of microbial contamination in the poultry industry, emphasizing this setting as a potential reservoir of microbial pathogens threatening human, animal, and environmental health. Additionally, this research helps to provide a sampling and analysis protocol proposal to evaluate the microbiological contamination in these facilities. Few articles were found reporting fungal contamination in poultry farms worldwide. In addition, information concerning fungal resistance profile and mycotoxin contamination remain scarce. Overall, a One Health approach should be incorporated in exposure assessments and the knowledge gaps identified in this paper should be addressed in further research.

Gomes, Bianca (ORCID:0000000262646072)↗

Hysteretic temperature sensitivity of wetland CH 4 fluxes explained by substrate availability and microbial activity

Methane (CH 4 ) emissions from wetlands are likely increasing and important in global climate change assessments. However, contemporary terrestrial biogeochemical model predictions of CH 4 emissions are very uncertain, at least in part due to prescribed temperature sensitivity of CH 4 production and emission. While statistically consistent apparent CH 4 emission temperature dependencies have been inferred from meta-analyses across microbial to ecosystem scales, year-round ecosystem-scale observations have contradicted that finding. Here, we show that apparent CH 4 emission temperature dependencies inferred from year-round chamber measurements exhibit substantial intra-seasonal variability, suggesting that using static temperature relations to predict CH 4 emissions is mechanistically flawed. Our model results indicate that such intra-seasonal variability is driven by substrate-mediated microbial and abiotic interactions: seasonal cycles in substrate availability favors CH 4 production later in the season, leading to hysteretic temperature sensitivity of CH 4 production and emission. Our findings demonstrate the uncertainty of inferring CH 4 emission or production rates from temperature alone and highlight the need to represent microbial and abiotic interactions in wetland biogeochemical models.

54 ENVIRONMENTAL SCIENCES↗

CompLaB v1.0: a scalable pore-scale model for flow, biogeochemistry, microbial metabolism, and biofilm dynamics

Abstract. Microbial activity and chemical reactions in porous media depend on the local conditions at the pore scale and can involve complex feedback with fluid flow and mass transport. We present a modeling framework that quantitatively accounts for the interactions between the bio(geo)chemical and physical processes and that can integrate genome-scale microbial metabolic information into a dynamically changing, spatially explicit representation of environmental conditions. The model couples a lattice Boltzmann implementation of Navier–Stokes (flow) and advection–diffusion-reaction (mass conservation) equations. Reaction formulations can include both kinetic rate expressions and flux balance analysis, thereby integrating reactive transport modeling and systems biology. We also show that the use of surrogate models such as neural network representations of in silico cell models can speed up computations significantly, facilitating applications to complex environmental systems. Parallelization enables simulations that resolve heterogeneity at multiple scales, and a cellular automaton module provides additional capabilities to simulate biofilm dynamics. The code thus constitutes a platform suitable for a range of environmental, engineering and – potentially – medical applications, in particular ones that involve the simulation of microbial dynamics.

58 GEOSCIENCES↗