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At least 829 records · Page 46

Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae

Abstract Anaerobic oxidation of methane (AOM) is a major biological process that reduces global methane emission to the atmosphere. Anaerobic methanotrophic archaea (ANME) mediate this process through the coupling of methane oxidation to different electron acceptors, or in concert with a syntrophic bacterial partner. Recently, ANME belonging to the archaeal family Methanoperedenaceae (formerly known as ANME-2d) were shown to be capable of AOM coupled to nitrate and iron reduction. Here, a freshwater sediment bioreactor fed with methane and Mn(IV) oxides (birnessite) resulted in a microbial community dominated by two novel members of the Methanoperedenaceae, with biochemical profiling of the system demonstrating Mn(IV)-dependent AOM. Genomic and transcriptomic analyses revealed the expression of key genes involved in methane oxidation and several shared multiheme c-type cytochromes (MHCs) that were differentially expressed, indicating the likely use of different extracellular electron transfer pathways. We propose the names “Candidatus Methanoperedens manganicus” and “Candidatus Methanoperedens manganireducens” for the two newly described Methanoperedenaceae species. This study demonstrates the ability of members of the Methanoperedenaceae to couple AOM to the reduction of Mn(IV) oxides, which suggests their potential role in linking methane and manganese cycling in the environment.

54 ENVIRONMENTAL SCIENCES↗

Prediction of Distributed River Sediment Respiration Rates Using Community-Generated Data and Machine Learning

River sediment microbial respiration is a key indicator of ecosystem functioning and the biogeochemical fluxes across this critical zone link surface and subsurface waters. As such, there is tremendous interest in measuring and mapping these respiration rates. Respiration observations are expensive and labor intensive; there is limited data available to the community. An open science, collaborative initiative is collecting samples for respiration rate analysis and multi-scale metadata; this evolving data set is being used for making machine learning (ML) predictions at unsampled sites to help inform continued community engagement. However, it is a challenge to find an optimum configuration for ML models to work with this feature-rich (i.e., 100+ possible input variables) data set. Here, we present results from a two-tiered approach to managing the analysis of this complex data set: (a) a stacked ensemble of models that automatically optimizes hyperparameters and manages the training of many models and (b) feature permutation importance to detect the most important features in the models. The major elements of this workflow are modular, portable, open, and cloud-based thus making this implementation a potential template for other applications. The models developed here predict that sediment organic matter chemistry is one of the most important features for predicting sediment respiration rate. Other larger-scale, important features fall into the categories of climatic, ecological, geological, and fluvial settings. Leveraging these larger-scale features to generate data-driven estimates of river sediment respiration rates reveals spatially consistent but heterogeneous patterns across the river network of the Columbia River Basin.

54 ENVIRONMENTAL SCIENCES↗

Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily

Abstract Hydrothermal vents have been key to our understanding of the limits of life, and the metabolic and phylogenetic diversity of thermophilic organisms. Here we used environmental metagenomics combined with analysis of physicochemical data and 16S rRNA gene amplicons to characterize the sediment-hosted microorganisms at the recently discovered Auka vents in the Gulf of California. We recovered 325 metagenome assembled genomes (MAGs) representing 54 phyla, over 30% of those currently known, showing the microbial community in Auka hydrothermal sediments is highly diverse. 16S rRNA gene amplicon screening of 224 sediment samples across the vent field indicates that the MAGs retrieved from a single site are representative of the microbial community in the vent field sediments. Metabolic reconstruction of a vent-specific, deeply branching clade within the Desulfobacterota suggests these organisms metabolize sulfur using novel octaheme cytochrome-c proteins related to hydroxylamine oxidoreductase. Community-wide comparison between Auka MAGs and MAGs from Guaymas Basin revealed a remarkable 20% species-level overlap, suggestive of long-distance species transfer over 400 km and subsequent sediment colonization. Optimal growth temperature prediction on the Auka MAGs, and thousands of reference genomes, shows that thermophily is a trait that has evolved frequently. Taken together, our Auka vent field results offer new perspectives on our understanding of hydrothermal vent microbiology.

54 ENVIRONMENTAL SCIENCES↗

Carbon balance in bioregenerative life support systems: some effects of system closure, waste management, and crop harvest index

In Advanced Life Support (ALS) systems with bioregenerative components, plant photosynthesis would be used to produce O2 and food, while removing CO2. Much of the plant biomass would be inedible and hence must be considered in waste management. This waste could be oxidized (e.g., incinerated or aerobically digested) to resupply CO2 to the plants, but this would not be needed unless the system were highly closed with regard to food. For example, in a partially closed system where some of the food is grown and some is imported, CO2 from oxidized waste when combined with crew and microbial respiration could exceed the CO2 removal capability of the plants. Moreover, it would consume some O2 produced from photosynthesis that could have been used by the crew. For partially closed systems it would be more appropriate to store or find other uses for the inedible biomass and excess carbon, such as generating soils or growing woody plants (e.g., dwarf fruit trees). Regardless of system closure, high harvest crops (i.e., crops with a high edible to total biomass ratio) would increase food production per unit area and O2 yields for systems where waste biomass is oxidized to recycle CO2. Such interlinking effects between the plants and waste treatment strategies point out the importance of oxidizing only that amount of waste needed to optimize system performance. Published by Elsevier Science Ltd on behalf of COSPAR.

NASA Discipline Life Support Systems↗

Cycling phosphorus on the Archean Earth: Part II. Phosphorus limitation on primary production in Archean ecosystems

Several lines of evidence point to low rates of net primary production (NPP) in Archean oceans. However, whether Archean NPP was limited by electron donors or nutrients, particularly phosphorus (P), and how these factors might have changed over a billion years of recorded Archean history, remains contentious. One major challenge is to understand quantitatively the biogeochemical cycling of P on the early Earth. In Part I of this series (Hao et al., 2020), we estimated the weathering flux of P to the oceans as a function of temporally increasing continental emergence and elevation through Archean time. In Part II, we conduct thermodynamic and kinetic simulations to understand key processes of P cycling within the Archean ocean, including seafloor weathering, recycling of organic P, the solubility and precipitation of secondary phosphate minerals, and the burial diagenesis of P precipitates. Our calculations suggest low solubilities of apatite minerals in Archean seawater, primarily due to nearly neutral pH and high levels of Ca. This low solubility, in turn, implies a negligible contribution of apatite dissolution to P bioavailability in Archean seawater. We also simulate the solubility limits of common secondary P-bearing minerals, showing that vivianite would have been the least soluble P mineral in ferruginous Archean seawater (0.1–0.3 µM), even at moderate supersaturation states (Ω = 100 or 1000). If vivianite precipitation was kinetically favorable by microbial activities and mineral adsorption, the sinking flux of P as vivianite in Archean seawater could have reached the modern sinking flux, implying that vivianite precipitation was a potentially major sink for P in Archean oceans. During burial diagenesis, however, vivianite in porewater would have become less stable than Ca-phosphates of lower solubility. At elevated temperatures (>100 °C) associated with burial diagenesis and low-grade metamorphism, vivianite is predicted to react irreversibly with calcite to form apatite. Optimistic assumptions about the recycling efficiency of P on the Archean Earth lead us to estimate that by the end of the eon the total flux of P (continental weathering + recycling) could have supported NPP at levels up to 7% of the modern. The total flux of P would have been much lower on the early and middle Archean Earth, whereas fluxes of electron donors could have been higher, suggesting very low productivity and P-limitation of marine ecosystems during much of the eon. Comparing our estimates of NPP as limited by P supply with the estimate by Ward et al. (2019), in which NPP was limited by electron donors and metabolic efficiency, there could have been a transition between P-limited productivity in the early to middle Archean to electron donor-limitation closer to the eon’s end (assuming no oxygenic photosynthesis). Once oxygenic photosynthesis reached ecological significance, probably near the end of the Archean, our estimated flux of P would allow rapid oxidation of atmosphere.

Vivianite↗

Surface Texture of Macroplastic Pollution in Streams Alters the Physical Structure and Diversity of Biofilm Communities

ABSTRACT Biofilms can develop on nearly any surface, and in aquatic ecosystems they are essential components of biogeochemical cycles and food webs. Plastic waste in waterways is a new type of surface for biofilm colonisation. To analyse the influence of plastic pollution on the development and diversity of microbial freshwater biofilms that colonised them, we incubated 388 cm 2 veneers of high‐density polyethylene (HDPE) with two veneer textures, smooth and rough, and tulip tree wood ( Liriodendron tulipifera ), in three rural headwater streams at the Savannah River Site (Aiken, SC, USA). We collected biofilms from veneers after 14, 28 and 56 days of incubation and analysed 16S rRNA genes and biofilm properties. We found that plastic negatively affected species richness of biofilms compared with wood, but that evenness was greatest on rough textured HDPE. Beta diversity was primarily influenced by stream site. Beta diversity differed more between wood and plastic veneers than with plastic surface texture and became more different over time. Wood had nine times more biomass than rough HDPE and 40 times more biomass than smooth HDPE. Given the projected increase of macroplastic pollution in aquatic ecosystems, our findings emphasise the need to further understand its effects on biofilm characteristics.

Lopez Avila, Fabiola [Odum School of Ecology Unive↗

The Study of Microbial Physiology Under Microoxic Conditions Is Critical but Neglected

ABSTRACT During the early evolution of life on Earth, the environment was largely free of molecular oxygen, and only anaerobic life existed. With the subsequent oxidation of oceans and the atmosphere, a wide range of environmental niches, ranging from anoxic to microoxic/hypoxic and oxic, developed. Despite this broad range of natural environments, microbiology as a field has focused on the physiology, metabolism, and genetics of aerobic microorganisms, with less attention paid to anaerobes and much less attention paid to microaerophiles. The disparity in studies between aerobic and anaerobic conditions is rampant in host‐associated systems, particularly in human health, and studies of microorganisms in intermediate oxygen conditions between fully aerobic and fully anoxic conditions are exceedingly rare. Studies on the physiological behaviour, metabolism, growth response, and drug susceptibility patterns of commensal and pathogenic organisms are almost totally neglected in microoxic conditions. Furthermore, microorganisms from microaerobic and microoxic ecosystems have been less robustly explored in terms of physiology, growth, and metabolism. In this work, we highlight the importance of understanding the physiological and metabolic behaviours of microorganisms under hypoxic or microoxic conditions.

Environmental Sciences & Ecology↗

Coupled abiotic-biotic cycling of nitrous oxide in tropical peatlands

Atmospheric nitrous oxide (N 2 O) is a potent greenhouse gas thought to be mainly derived from microbial metabolism as part of the denitrification pathway. Here we report that in unexplored peat soils of Central and South America, N 2 O production can be driven by abiotic reactions (≤98%) highly competitive to their enzymatic counterparts. Extracted soil iron positively correlated with in situ abiotic N 2 O production determined by isotopic tracers. Moreover, we found that microbial N 2 O reduction accompanied abiotic production, essentially closing a coupled abiotic-biotic N 2 O cycle. Anaerobic N 2 O consumption occurred ubiquitously (pH 6.4–3.7), with proportions of diverse clade II N 2 O reducers increasing with consumption rates. Our findings show that denitrification in tropical peat soils is not a purely biological process but rather a ‘mosaic’ of abiotic and biotic reduction reactions. Here, we predict that hydrological and temperature fluctuations differentially affect abiotic and biotic drivers and further contribute to the high N 2 O flux variation in the region.

54 ENVIRONMENTAL SCIENCES↗

Baltic Sea coastal sediment-bound eukaryotes have increased year-round activities under predicted climate change related warming

Climate change related warming is a serious environmental problem attributed to anthropogenic activities, causing ocean water temperatures to rise in the coastal marine ecosystem since the last century. This particularly affects benthic microbial communities, which are crucial for biogeochemical cycles. While bacterial communities have received considerable scientific attention, the benthic eukaryotic community response to climate change remains relatively overlooked. In this study, sediments were sampled from a heated (average 5°C increase over the whole year for over 50 years) and a control (contemporary conditions) Baltic Sea bay during four different seasons across a year. RNA transcript counts were then used to investigate eukaryotic community changes under long-term warming. The composition of active species in the heated and control bay sediment eukaryotic communities differed, which was mainly attributed to salinity and temperature. The family level RNA transcript alpha diversity in the heated bay was higher during May but lower in November, compared with the control bay, suggesting altered seasonal activity patterns and dynamics. In addition, structures of the active eukaryotic communities varied between the two bays during the same season. Hence, this study revealed that long-term warming can change seasonality in eukaryotic diversity patterns. Relative abundances and transcript expression comparisons between bays suggested that some taxa that now have lower mRNA transcripts numbers could be favored by future warming. Furthermore, long-term warming can lead to a more active metabolism in these communities throughout the year, such as higher transcript numbers associated with diatom energy production and protein synthesis in the heated bay during winter. In all, these data can help predict how future global warming will affect the ecology and metabolism of eukaryotic community in coastal sediments.

59 BASIC BIOLOGICAL SCIENCES↗

Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions

Polysaccharide utilization loci (PULs) are co-regulated bacterial genes that sense nutrients and enable glycan digestion. Human gut microbiome members, notably Bacteroides, contain numerous PULs that enable glycan utilization and shape ecological dynamics. To investigate the role of PULs on fitness and inter-species interactions, we develop a CRISPR-based genome editing tool to study 23 PULs in Bacteroides uniformis (BU). BU PULs show distinct glycan-degrading functions and transcriptional coordination that enables the population to adapt upon loss of other PULs. Exploiting a BU mutant barcoding strategy, we demonstrate that in vitro fitness and BU colonization in the murine gut are enhanced by deletion of specific PULs and modulated by glycan availability. PULs mediate glycan-dependent interactions with butyrate producers that depend on the degradation mechanism and glycan utilization ability of the butyrate producer. Thus, PULs determine community dynamics and butyrate production and provide a selective advantage or disadvantage depending on the nutritional landscape.

59 BASIC BIOLOGICAL SCIENCES↗

Natural soil microbiome variation affects spring foliar phenology with consequences for plant productivity and climate-driven range shifts

Identifying the potential for natural soil microbial communities to predictably affect complex plant traits is an important frontier in climate change research. Plant phenology varies with environmental and genetic factors, but few studies have examined if the soil microbiome interacts with plant population differentiation to affect phenology and ecosystem function. We compared soil microbial variation in a widespread tree species (Populus angustifolia) with different soil inoculum treatments in a common garden environment to test how the soil microbiome affects spring foliar phenology and subsequent biomass growth. We hypothesized and show that: 1) soil bacterial and fungal communities vary with tree conditioning from different populations and elevations, 2) this soil community variation influences patterns of foliar phenology and plant growth across populations and elevation gradients, and 3) transferring lower elevation plant genotypes to higher elevation soil communities delayed foliar phenology, thereby shortening the growing season and reducing annual biomass production. Our findings show the importance of plant-soil interactions that help shape the timing of tree foliar phenology and productivity. Here, these geographic patterns in plant population x microbiome interactions also broaden our understanding of how soil communities impact plant phenotypic variation across key climate change gradients, with consequences for ecosystem functioning.

59 BASIC BIOLOGICAL SCIENCES↗

Stable carbon isotope fractionation by sulfate-reducing bacteria

Biogeochemical transformations occurring in the anoxic zones of stratified sedimentary microbial communities can profoundly influence the isotopic and organic signatures preserved in the fossil record. Accordingly, we have determined carbon isotope discrimination that is associated with both heterotrophic and lithotrophic growth of pure cultures of sulfate-reducing bacteria (SRB). For heterotrophic-growth experiments, substrate consumption was monitored to completion. Sealed vessels containing SRB cultures were harvested at different time intervals, and delta(13)C values were determined for gaseous CO(2), organic substrates, and products such as biomass. For three of the four SRB, carbon isotope effects between the substrates, acetate or lactate and CO(2), and the cell biomass were small, ranging from 0 to 2 per thousand. However, for Desulfotomaculum acetoxidans, the carbon incorporated into biomass was isotopically heavier than the available substrates by 8 to 9 per thousand. SRB grown lithoautotrophically consumed less than 3% of the available CO(2) and exhibited substantial discrimination (calculated as isotope fractionation factors [alpha]), as follows: for Desulfobacterium autotrophicum, alpha values ranged from 1.0100 to 1.0123; for Desulfobacter hydrogenophilus, the alpha value was 0.0138, and for Desulfotomaculum acetoxidans, the alpha value was 1.0310. Mixotrophic growth of Desulfovibrio desulfuricans on acetate and CO(2) resulted in biomass with a delta(13)C composition intermediate to that of the substrates. The extent of fractionation depended on which enzymatic pathways were used, the direction in which the pathways operated, and the growth rate, but fractionation was not dependent on the growth phase. To the extent that environmental conditions affect the availability of organic substrates (e.g., acetate) and reducing power (e.g., H(2)), ecological forces can also influence carbon isotope discrimination by SRB.

Deltaproteobacteria/growth & development/metabolis↗

Differences in spore size and atmospheric survival shape stark contrasts in the dispersal dynamics of two closely related fungal pathogens

A frequently ignored but critical aspect of microbial dispersal is survival in the atmosphere. Here, we exposed spores of two closely related, morphologically dissimilar, and economically important fungal pathogens to typical atmospheric environments and modeled their movement in the troposphere. Alternaria solani conidia are nearly 10 times larger than A. alternata conidia, but in our experiments, most died within 24 h, while over half of A. alternata conidia remained viable on day 12. Next, we modeled the movement of spores across North America. We predict 99% of the larger A. solani conidia settle within 24 h, with a maximum dispersal distance of 100 km. By contrast, most A. alternata conidia remain airborne for more than 12 days, and dispersal over long distances(2000 km) is likely. Counterintuitively, the larger A. solani conidia survive poorly, as compared to smaller A. alternata conidia, but also land sooner and move over shorter distances.

59 BASIC BIOLOGICAL SCIENCES↗

Aged and unaged pine wood pyrogenic organic matter: mineralization, elemental analysis and spectroscopy data (February 2020)

In this study, we used a pyrogenic organic matter (PyOM) degrading Streptomyces isolate – a globally common soil bacterium – to investigate the effects of physical (freeze-thaw and wet-dry), chemical (oxidation), and biological (microbial community incubation) ageing on the chemical properties and mineralizability of 350°C and 550°C pine wood PyOM. We used Fourier Transform Infrared spectroscopy (FTIR) and elemental analysis to characterize the aged and unaged PyOM, and cavity ring-down spectroscopy to trace CO2 emissions. The carbon (C) mineralization data from incubation of aged and unaged PyOM with the isolate are provided in co2cmg_picarro_022020.csv. This dataset contains raw carbon dioxide (CO2) data measured on the cavity ring-down spectroscopy over 1 month of incubation. The dataset also includes processed data such as cumulative CO2 emitted over multiple cycles of measurement and CO2 values normalized by the total carbon content in each PyOM treatment. The carbon, hydrogen and nitrogen elemental content of aged and unaged 350°C and 550°C pine wood PyOM are provided in CHN_pyom.csv. The relative peak heights measured during the FTIR analysis of aged and unaged PyOM are provided in ftir_peaks_rel.csv.

54 ENVIRONMENTAL SCIENCES↗

Engineering strategies for the design of plant nutrient delivery systems for use in space: approaches to countering microbiological contamination

Microbiological contamination of crops within space-based plant growth research chambers has been postulated as a potentially significant problem. Microbial infestations; fouling of Nutrient Delivery System (NDS) fluid loops; and the formation of biofilms have been suggested as the most obvious and important manifestations of the problem. Strict sanitation and quarantine procedures will reduce, but not eliminate, microbial species introduced into plant growth systems in space habitats. Microorganisms transported into space most likely will occur as surface contaminants on spacecraft components, equipment, the crew, and plant-propagative materials. Illustrations of the potential magnitude of the microbiological contamination issue will be drawn from the literature and from documentation of laboratory and commercial field experience. Engineering strategies for limiting contamination and for the development of countermeasures will be described. Microbiological control technologies and NDS hardware will be discussed. Configurations appropriate for microgravity research facilities, as well as anticipated bio-regenerative life support system implementations, will be explored. An efficiently designed NDS, capable of adequately meeting the environmental needs of crop plants in space, is considered to be critical in both the research and operational domains. Recommended experiments, tests, and technology developments, structured to allow the development of prudent engineering solutions also will be presented.

NASA Discipline Number 61-10↗

Surface-active antibiotic production as a multifunctional adaptation for postfire microorganisms

Abstract Wildfires affect soils in multiple ways, leading to numerous challenges for colonizing microorganisms. Although it is thought that fire-adapted microorganisms lie at the forefront of postfire ecosystem recovery, the specific strategies that these organisms use to thrive in burned soils remain largely unknown. Through bioactivity screening of bacterial isolates from burned soils, we discovered that several Paraburkholderia spp. isolates produced a set of unusual rhamnolipid surfactants with a natural methyl ester modification. These rhamnolipid methyl esters (RLMEs) exhibited enhanced antimicrobial activity against other postfire microbial isolates, including pyrophilous Pyronema fungi and Amycolatopsis bacteria, compared to the typical rhamnolipids made by organisms such as Pseudomonas spp. RLMEs also showed enhanced surfactant properties and facilitated bacterial motility on agar surfaces. In vitro assays further demonstrated that RLMEs improved aqueous solubilization of polycyclic aromatic hydrocarbons, which are potential carbon sources found in char. Identification of the rhamnolipid biosynthesis genes in the postfire isolate, Paraburkholderia kirstenboschensis str. F3, led to the discovery of rhlM, whose gene product is responsible for the unique methylation of rhamnolipid substrates. RhlM is the first characterized bacterial representative of a large class of integral membrane methyltransferases that are widespread in bacteria. These results indicate multiple roles for RLMEs in the postfire lifestyle of Paraburkholderia isolates, including enhanced dispersal, solubilization of potential nutrients, and inhibition of competitors. Our findings shed new light on the chemical adaptations that bacteria employ to navigate, grow, and outcompete other soil community members in postfire environments.

59 BASIC BIOLOGICAL SCIENCES↗

Comparing western (Megascops kennicottii) and whiskered (M. trichopsis) screech-owl microbiomes in southern Arizona using a novel 16S rRNA sequencing method

Microbiomes are essential to a host’s physiology and health. Despite the overall importance of microbiomes to animal health, they remain understudied in wildlife. Microbiomes function as physical barriers to invading pathogens, and changes in the diversity or composition of microbes within a host may disrupt this barrier. In order to use microbiomes in wildlife ecology, knowledge of the natural variation within and among species is essential. We compare the diversity and composition of two avian species that share the same habitat and niche in our study area, the western screech-owl (Megascops kennicottii) and the whiskered screech-owl (M. trichopsis). We used a targeted 16S sequencing method to improve the taxonomic resolution of microbiomes. We found similar measures of alpha diversity between species and sample types (cloacal samples vs. fecal samples). However, there were significant differences in bacterial species richness among nestlings from different nest boxes, and the composition differed between the two bird species and among nestlings from different nest boxes. Western screech-owls had more variation in alpha diversity and composition and had fewer bacterial species in their core microbiome than whiskered screech-owls. Siblings are likely to yield similar findings for microbiomes; thus, sampling nestlings from different nests may be most informative for monitoring population-level changes.

59 BASIC BIOLOGICAL SCIENCES↗

Spatial controls of methane uptake in upland soils across climatic and geological regions in Greenland

Abstract In the Arctic, the spatiotemporal variation of net methane uptake in upland soils depends on unresolved interactive controls between edaphic and microbial factors not yet included in current models, underpinning the uncertainty of upscaling the Arctic methane budget. Here we show that upland soils in Greenland are consistent methane sinks (−1.83 ± 0.19 nmol methane g −1 dw d −1 ) across a N-S (64–83 °N) pedoclimatic transect. We demonstrate that methane oxidizers abundance, soil pH, and available soil copper are important controls on the spatial variation in methane oxidation. We revised a soil biogeochemical model with a high-resolution land classification and meteorological data for Greenland and tested it against our methane uptake measurements. The model simulated well the magnitudes of observed methane uptake but not the spatial variation across all sites. This work provides novel insights into the controls of methane uptake, which are critical for the accuracy of methane budgets.

Environmental Sciences & Ecology↗