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At least 361 records · Page 20

Quantitative stable isotope probing (qSIP) and cross-domain networks reveal bacterial-fungal interactions in the hyphosphere

Interactions between fungi and bacteria have the potential to substantially influence soil carbon dynamics in soil, but we have yet to fully identify these interactions and partners in their natural environment. In this study, we stacked two powerful methods, 13 C quantitative stable isotope probing (qSIP) and cross-domain co-occurrence network, to identify interacting fungi and bacteria in a California grassland soil. We used in-field whole plant 13 CO 2 labeling along with sand-filled ingrowth bags (that trap fungi and hyphae-associated bacteria) to amplify the signal of fungal-bacterial interactions, separate from the bulk soil background. We found a total of 54 bacterial ASVs and 9 fungal OTUs that were significantly 13 C-enriched. These were saprotrophic and biotrophic fungi, and motile, sometimes predatory bacteria. Among these, 70% of all 13 C-enriched bacteria identified were motile. Notably, we detected fungal-bacterial network links between a fungal OTU of the genus Alternaria and several bacterial ASVs of the genera Bacteriovorax, Mucilaginibacter, and Flavobacterium, providing empirical evidence of their direct interactions through C exchange. We observed a strong positive co-occurrence pattern between predatory bacteria of the phylum Bdellovibrionota and fungal OTUs, suggesting the transfer of C across the soil food web. To date, our ability to associate microbial co-occurrence network patterns with biological interactions is limited, but the incorporation of qSIP allowed us to more precisely detect interacting partners by narrowing in on the taxa that were actively incorporating plant-fixed, fungal-transported labeled substrates. Together, these approaches can help build a mechanistic understanding of the complex nature of fungal-bacterial interactions in soil.

59 BASIC BIOLOGICAL SCIENCES↗

Estimation of effective hydrologic properties of soils from observations of vegetation density

An existing one-dimensional model of the annual water balance is reviewed. Slight improvements are made in the method of calculating the bare soil component of evaporation, and in the way surface retention is handled. A natural selection hypothesis, which specifies the equilibrium vegetation density for a given, water limited, climate-soil system, is verified through comparisons with observed data and is employed in the annual water balance of watersheds in Clinton, Ma., and Santa Paula, Ca., to estimate effective areal average soil properties. Comparison of CDF's of annual basin yield derived using these soil properties with observed CDF's provides excellent verification of the soil-selection procedure. This method of parameterization of the land surface should be useful with present global circulation models, enabling them to account for both the non-linearity in the relationship between soil moisture flux and soil moisture concentration, and the variability of soil properties from place to place over the Earth's surface.

Tellers, T. E.↗

Volatile metal deposits on lunar soils: Relation to volcanism

Parallel leaching and volatilization experiments conducted on lunar samples and similar experiments on sphalerite do not supply the information needed to resolve the question of the chemical nature of pb 204, Zn, Bi and Tl deposits on lunar soil surfaces. It is proposed that in Apollo 17 mare and terra soils and fractions of pb 204, Zn and Tl that are insoluble under mild, hot pH 5HNO3, leaching conditions and involatile at 600 C were originally surface deposits which became immobilized by migration into the silicate substrate or by chemisorption. Only Bi is predominantly indigenous. The implication is also that the soils over their respective times of evolution were exposed to heavy metal vapors or that an episodic exposure occurred after they had evolved. A sequence of events is proposed to account for orange 74220 and black 74001 glasses by lava fountaining and for soil 74241 as tephra from an explosive volcanic eruption.

Reed, G. W., Jr.↗

Volatile metal deposits on lunar soils - Relation to volcanism

Parallel leaching and volatilization experiments conducted on lunar samples and similar experiments on sphalerite do not supply the information needed to resolve the question of the chemical nature of Pb-204, Zn, Bi, and Tl deposits on lunar soil surfaces. It is proposed that in Apollo 17 mare and terra soils the fractions of Pb-204, Zn, and Tl that are insoluble under mild, hot pH 5 HNO3, leaching conditions and involatile at 600 C were originally surface deposits which became immobilized by migration into the silicate substrate or by chemisorption. Most of the Bi does not seem to be the result of such a deposit. The implication is also that the soils, over their respective times of evolution, were exposed to heavy metal vapors or that an episodic exposure occurred after they had evolved. A sequence of events is proposed to account for orange 74220 and black 74001 glasses by lava fountaining and for soil 74241 as tephra from an explosive volcanic eruption.

Reed, G. W., Jr.↗

Investigation of indigenous water, salt and soil for solar ponds

The existence of salt-gradient solar ponds in nature is a strong indication that the successful exploitation of this phenomenon must account adequately for the influences of the local setting. Sun, weather and other general factors are treated elsewhere. This paper deals with water, salt, and soil. A general methodology for evaluating and, where feasible, adjusting the effects of these elements is under development. Eight essential solar pond characteristics have been identified, along with a variety of their dependencies upon properties of water, salt and soil. The comprehensive methodology, when fully developed, will include laboratory investigation in such diverse areas as brine physical chemistry, light transmission, water treatment, brine-soil interactions, sealants, and others. With the Salton Sea solar pond investigation as an example, some methods under development will be described.

Marsh, H. E.↗

Divergent accumulation of amino sugars and lignins mediated by soil functional carbon pools under tropical forest conversion

Tropical primary forests are being destroyed at an alarming rate and converted for other land uses which is expected to greatly influence soil carbon (C) cycling. However, our understanding of how tropical forest conversions affect the accumulation of compounds in soil functional C pools remains unclear. Here, we collected soils from primary forests (PF), secondary forests (SF), oil-palm (OP), and rubber plantations (RP), and assessed the accumulation of plant- and microbial-derived compounds within soil organic carbon (SOC), particulate (POC) and mineral-associated (MAOC) organic C. PF conversion to RP greatly decreased SOC, POC, and MAOC concentrations, whereas conversion to SF increased POC concentrations and decreased MAOC concentrations, and conversion to OP only increased POC concentrations. PF conversion to RP decreased lignin concentrations and increased amino sugar concentrations in SOC pools which increased the stability of SOC, whereas conversion to SF only increased the lignin concentrations in POC, and conversion to OP just increased lignin concentrations in POC and decreased it in MAOC. We observed divergent dynamics of amino sugars (decrease) and lignin (increase) in SOC with increasing SOC. Only lignin concentrations increased in POC with increasing POC and amino sugars concentrations decreased in MAOC with increasing MAOC. Conversion to RP significantly decreased soil enzyme activities and microbial biomasses. Lignin accumulation was associated with microbial properties, whereas amino sugar accumulation was mainly associated with soil nutrients and stoichiometries. These results suggest that the divergent accumulation of plant- and microbial-derived C in SOC was delivered by the distribution and original composition of functional C pools under forest conversions. Forest conversions changed the formation and stabilization processes of SOC in the long run which was associated with converted plantations and management. As a result, the important roles of soil nutrients and stoichiometry also provide a natural-based solution to enhance SOC sequestration via nutrient management in tropical forests.

59 BASIC BIOLOGICAL SCIENCES↗

Dissection of Carbon and Nitrogen Cycling in Post-Fire Soil Environments using a Genome- Informed Experimental Community (Final Technical Report)

Wildfires are a natural part of many forest ecosystems, with globally important carbon (C) storage and nutrient cycling consequences, and they are increasing in frequency and severity in Western North America. Forest fires affect soil C stocks in complex ways; some C is released into the atmosphere through combustion, while a large percentage of the C is added to the soil in the form of pyrogenic organic matter. Worldwide, it is estimated that 16% of soil organic matter is pyrogenic, while locally, this number may be as high as 80%. Understanding how wildfires affect soil organic matter cycling requires understanding how microbes respond to pyrogenic organic matter and other post-fire soil conditions. However, our understanding of microbial interactions within post-fire soil was in its infancy at the time of our proposal. Outstanding questions included: Which microbes are capable of degrading pyrogenic organic matter? What are the relevant genes and metabolites associated with this degradation? What are the key interactions among post-fire microbes? Key highlights of outcomes supported by this grant included training eleven early-career scientists and two early-career PIs, publication of twelve peer-reviewed papers, cross-lab collaborations that empowered complex scientific approaches, the development of an open-source automated gas sampler to drive novel insights in C cycling, enhanced understanding of post-fire microbial community dynamics, and novel genetic and molecular insights into microbial responses to fire.

54 ENVIRONMENTAL SCIENCES↗

Fungal hyphae develop where titanomagnetite inclusions reach the surface of basalt grains

Nutrient foraging by fungi weathers rocks by mechanical and biochemical processes. Distinguishing fungal-driven transformation from abiotic mechanisms in soil remains a challenge due to complexities within natural field environments. We examined the role of fungal hyphae in the incipient weathering of granulated basalt from a three-year field experiment in a mixed hardwood-pine forest (S. Carolina) to identify alteration at the nanometer to micron scales based on microscopy-tomography analyses. Investigations of fungal-grain contacts revealed (i) a hypha-biofilm-basaltic glass interface coinciding with titanomagnetite inclusions exposed on the grain surface and embedded in the glass matrix and (ii) native dendritic and subhedral titanomagnetite inclusions in the upper 1–2 µm of the grain surface that spanned the length of the fungal-grain interface. We provide evidence of submicron basaltic glass dissolution occurring at a fungal-grain contact in a soil field setting. An example of how fungal-mediated weathering can be distinguished from abiotic mechanisms in the field was demonstrated by observing hyphal selective occupation and hydrolysis of glass-titanomagnetite surfaces. We hypothesize that the fungi were drawn to basaltic glass-titanomagnetite boundaries given that titanomagnetite exposed on or very near grain surfaces represents a source of iron to microbes. Furthermore, glass is energetically favorable to weathering in the presence of titanomagnetite. Our observations demonstrate that fungi interact with and transform basaltic substrates over a three-year time scale in field environments, which is central to understanding the rates and pathways of biogeochemical reactions related to nuclear waste disposal, geologic carbon storage, nutrient cycling, cultural artifact preservation, and soil-formation processes.

58 GEOSCIENCES↗

Biological Carbon Sequestration for Climate and Soil Health

The United States recently launched the Net Zero World Initiative on decarbonization. As temperatures and sea levels rise, strong action is needed to mitigate high atmospheric CO 2 levels. In response to this need, a joint workshop between the US Department of Energy’s Oak Ridge National Laboratory (ORNL) and Lawrence Berkeley National Laboratory (LBNL) was convened to assess the challenges and opportunities within biological carbon (C) capture. The virtual workshop on Biological Carbon Sequestration for Climate and Soil Health focused on three aspects of biological C capture research: natural systems, engineered systems, and modeling. For this workshop, the scope of natural systems included unmanaged (e.g., grasslands, wetlands, natural forests) and managed (e.g., agricultural lands, commercial forests, forest biofuels) ecosystems. The engineered systems group covered topics in genetically modified plants and microbes, synthetic microbiomes, and altered plant–microbe interactions for enhancing C capture, storage, and utilization. The modeling group focused on computational tools and data collection to predict and assess the effectiveness of new biocarbon sequestration advances. Participant expertise included plant and microbial systems biology, synthetic biology, soil biogeochemistry, and techno-economic analysis. Together, participants outlined key scientific advances in support of biological C capture and storage. Among the major findings of the meeting were the need to better measure C flux within natural, agricultural, and fabricated ecosystems for experimentation; better understand the role of soil composition, plant roots, and the rhizosphere (i.e., the soil surrounding the plant root) in the underground storage of organic C; and design plant–microbe systems for maximal C storage.

54 ENVIRONMENTAL SCIENCES↗

Seasonal-to-Interannual Variability and Land Surface Processes

Atmospheric chaos severely limits the predictability of precipitation on subseasonal to interannual timescales. Hope for accurate long-term precipitation forecasts lies with simulating atmospheric response to components of the Earth system, such as the ocean, that can be predicted beyond a couple of weeks. Indeed, seasonal forecasts centers now rely heavily on forecasts of ocean circulation. Soil moisture, another slow component of the Earth system, is relatively ignored by the operational seasonal forecasting community. It is starting, however, to garner more attention. Soil moisture anomalies can persist for months. Because these anomalies can have a strong impact on evaporation and other surface energy fluxes, and because the atmosphere may respond consistently to anomalies in the surface fluxes, an accurate soil moisture initialization in a forecast system has the potential to provide additional forecast skill. This potential has motivated a number of atmospheric general circulation model (AGCM) studies of soil moisture and its contribution to variability in the climate system. Some of these studies even suggest that in continental midlatitudes during summer, oceanic impacts on precipitation are quite small relative to soil moisture impacts. The model results, though, are strongly model-dependent, with some models showing large impacts and others showing almost none at all. A validation of the model results with observations thus naturally suggests itself, but this is exceedingly difficult. The necessary contemporaneous soil moisture, evaporation, and precipitation measurements at the large scale are virtually non-existent, and even if they did exist, showing statistically that soil moisture affects rainfall would be difficult because the other direction of causality - wherein rainfall affects soil moisture - is unquestionably active and is almost certainly dominant. Nevertheless, joint analyses of observations and AGCM results do reveal some suggestions of land-atmosphere feedback in the observational record, suggestions that soil moisture can affect precipitation over seasonal timescales and across certain large continental areas. The strength of this observed feedback in nature is not large but is still significant enough to be potentially useful, e.g., for forecasts. This talk will address all of these issues. It will begin with a brief overview of land surface modeling in atmospheric models but will then focus on recent research - using both observations and models - into the impact of land surface processes on variability in the climate system.

Koster, Randal↗

Laboratory Investigations

The primary objectives were to examine the site-specific physical, chemical, and biological factors that impact construction, durability and performance of the proposed 5-MW (sub e) solar pond system at the Salton Sea. The interactions of the water, salt, and soil of the site and on material compatibility were examined. Potential interactions of the water/brine and soil are particularly important because the pond will utilize the naturally occurring clays as a bottom seal. Although there is a considerable and growing solar pond literature, little written information deals with the important site-specific investigations of water, salt, and soil. Therefore, technical effort was directed toward identifying the factors that should be investigated and determining methods of investigation. As a result, a by-product was the development of an approach for site-specific investigations and some specific methodologies. This development should continue in order to establish a generic approach for evaluating the suitability of any site for the construction of large-scale solar ponds.

Source record↗

Multiple elements of soil biodiversity drive ecosystem functions across biomes

The role of soil biodiversity in regulating multiple ecosystem functions is poorly understood, limiting our ability to predict how soil biodiversity loss might affect human wellbeing and ecosystem sustainability. Furthermore, combining a global observational study with an experimental microcosm study, we provide evidence that soil biodiversity (bacteria, fungi, protists and invertebrates) is significantly and positively associated with multiple ecosystem functions. These functions include nutrient cycling, decomposition, plant production, and reduced potential for pathogenicity and belowground biological warfare. Our findings also reveal the context dependency of such relationships and the importance of the connectedness, biodiversity and nature of the globally distributed dominant phylotypes within the soil network in maintaining multiple functions. Moreover, our results suggest that the positive association between plant diversity and multifunctionality across biomes is indirectly driven by soil biodiversity. Together, our results provide insights into the importance of soil biodiversity for maintaining soil functionality locally and across biomes, as well as providing strong support for the inclusion of soil biodiversity in conservation and management programmes.

54 ENVIRONMENTAL SCIENCES↗

Multi-scale Analysis of Surface Heterogeneity Induced Convection on Isentropic Coordinates

This research uses semi-idealized simulations to investigate multi-scale processes induced by the heterogeneity of soil moisture observed during the 2016 Holistic Interactions of Shallow Clouds, Aerosols, and Land-Ecosystems (HI-SCALE) field campaign. The semi-idealized simulations have realistic land heterogeneity, but large-scale winds are removed. Analysis on isentropic coordinates enables the tracking of circulation that transports energy vertically and facilitates the identification of the primary convective processes induced by realistic land heterogeneity. The isentropes associated with upward motion are found to connect the ground characterized by high latent heat flux to cloud bases directly over the ground with high sensible heat flux, while isentropes associated with downward motion connect precipitation to the ground characterized by high sensible heat fluxes. The mixing of dry, warm parcels ascending from the ground with high sensible heat fluxes and moist parcels from high latent heat regions leads to cloud formation. This new mechanism explains how soil moisture heterogeneity provides the key ingredients such as buoyancy and moisture for shallow cloud formation. We also found that the sub-mesoscale dominates upward energy transport in the boundary layer, while mesoscale circulations contribute to vertical energy transport above the boundary layer. Our novel method better illustrates and elucidates the nature of land atmospheric interactions under irregular and realistic soil moisture patterns.

54 ENVIRONMENTAL SCIENCES↗

Evaluating a Laboratory Flume Microbiome as a Window Into Natural Riverbed Biogeochemistry

Riverbeds are hotspots for microbially-mediated reactions that exhibit pronounced variability in space and time. It is challenging to resolve biogeochemical mechanisms in natural riverbeds, as uncontrolled settings complicate data collection and interpretation. To overcome these challenges, laboratory flumes are often used as proxies for natural riverbed systems. Flumes capture spatiotemporal variability and thus allow for controlled investigations of riverbed biogeochemistry. These investigations implicitly rely on the assumption that the flume microbiome is similar to the microbiome of natural riverbeds. However, this assumption has not been tested and it is unknown how the microbiome of a flume compares to natural aquatic settings, including riverbeds. To evaluate the fundamental assumption that a flume hosts a microbiome similar to natural riverbed systems, we used 16s rRNA gene sequencing and publicly available data to compare the sediment microbiome of a single large laboratory flume to a wide variety of natural ecosystems including lake and marine sediments, river, lake, hyporheic, soil, and marine water, and bank and wetland soils. Richness and Shannon diversity metrics, analyses of variance, Bray-Curtis dissimilarity, and analysis of the common microbiomes between flume and river sediment all indicated that the flume microbiome more closely resembled natural riverbed sediments than other ecosystems, supporting the use of flume experiments for investigating natural microbially-mediated biogeochemical processes in riverbeds.

54 ENVIRONMENTAL SCIENCES↗

35-GHz Measurements of Carbon Dioxide Crystals

In order to maximize our knowledge of the martian polar caps, it is important to compare and contrast the behavior of both frozen H2O and CO2 in different parts of the electromagnetic spectrum. Relatively little attention has been given, thus far, to observing the thermal microwave part of the spectrum. In this experiment, passive microwave radiation emanating from within a 33-cm snowpack was measured with a 35-GHz hand-held radiometer, and in addition to the natural snow measurements, the radiometer was used to measure the microwave emission and scattering from layers of manufactured CO2 (dry ice) crystals. A 1 square meter plate of aluminum sheet metal was positioned beneath the natural snow so that microwave emissions from the underlying soil layers would be minimized. 35 GHz measurements of this plate were made through the 33-cm snowpack. Layers of the snow were removed and measurements were repeated for the diminishing snowpack until the bare plate was in view. Then, 9 cm of CO2 crystals were deposited onto the sheet-metal plate, and as was the case for the natural snow, hand-held measurements were made each time the thickness of the deposit was altered. These CO2 crystals were -0.65 cm in diameter and were cylindrical. The temperature of the dry ice was -76 C, whereas the temperature at the top of the snowpack was -1.9 C (the air temperature was -3 C). Two additional 9-cm increments were placed on top of the existing CO2 crystals, resulting in a total thickness of 27 cm of dry ice. After this series of measurements was made, the CO2 crystals were then placed on top of the snowpack, and as before, measurements were made using the 35-GHz radiometer. As a final part of this experiment, soil particles were spread on top of the dry ice, and once again, microwave measurements were made with the 35-GHz radiometer.

Foster, J.↗

Copper availability governs nitrous oxide accumulation in wetland soils and stream sediments

Denitrification is microbially-mediated through enzymes containing metal cofactors. Laboratory studies of pure cultures have highlighted that the availability of Cu, required for the multicopper enzyme nitrous oxide reductase, can limit N2O reduction. However, in natural aquatic systems, such as wetlands and hyporheic zones in stream beds, the role of Cu in controlling denitrification remains incompletely understood. In this study, we collected soils and sediments from three natural environments -- riparian wetlands, marsh wetlands, and a stream -- to investigate their nitrogen species transformation activity at background Cu levels and different supplemented Cu loadings. All of the systems contained solid-phase associated Cu below or around geological levels (40 - 280 nmol g-1) and exhibited low dissolved Cu (3-50 nM), which made them appropriate sites for evaluating the effect of limited Cu availability on denitrification. In laboratory incubation experiments, high concentrations of N2O accumulated in all microcosms lacking Cu amendment except for one stream sediment sample. With Cu added to provide dissolved concentrations at trace levels (10-300 nM), reduction rate of N2O to N 2 in the wetland soils and stream sediments was enhanced. A kinetic model could account for the trends in nitrogen species by combining the reactions for microbial reduction of NO 3 - to NO 2 -/N 2 O/N 2 and abiotic reduction of NO 2 - to N 2 . The model revealed that the rate of N 2 O to N 2 conversion increased significantly in the presence of Cu. For riparian wetland soils and stream sediments, the kinetic model also suggested that overall denitrification is driven by abiotic reduction of NO2- in the presence of inorganic electron donors. This study demonstrated that natural aquatic systems containing Cu at concentrations less than or equal to crustal abundances may display incomplete reduction of N 2 O to N 2 that would cause N 2 O accumulation and release to the atmosphere.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

Background: Viruses impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral communities have been identified, with a global distribution seemingly driven by multiple biotic and abiotic factors, especially soil temperature and moisture. However, our current understanding of the stability of soil viral communities across time and their response to strong seasonal changes in environmental parameters remains limited. Here, we investigated the diversity and activity of environmental soil DNA and RNA viruses, focusing especially on bacteriophages, across dynamics’ seasonal changes in a snow-dominated mountainous watershed by examining paired metagenomes and metatranscriptomes. Results: We identified a large number of DNA and RNA viruses taxonomically divergent from existing environmental viruses, including a significant proportion of fungal RNA viruses, and a large and unsuspected diversity of positive single-stranded RNA phages ( Leviviricetes ), highlighting the under-characterization of the global soil virosphere. Among these, we were able to distinguish subsets of active DNA and RNA phages that changed across seasons, consistent with a “seed-bank” viral community structure in which new phage activity, for example, replication and host lysis, is sequentially triggered by changes in environmental conditions. At the population level, we further identified virus-host dynamics matching two existing ecological models: “Kill-The-Winner” which proposes that lytic phages are actively infecting abundant bacteria, and “Piggyback-The-Persistent” which argues that when the host is growing slowly, it is more beneficial to remain in a dormant state. The former was associated with summer months of high and rapid microbial activity, and the latter with winter months of limited and slow host growth. Conclusion: Taken together, these results suggest that the high diversity of viruses in soils is likely associated with a broad range of host interaction types each adapted to specific host ecological strategies and environmental conditions. As our understanding of how environmental and host factors drive viral activity in soil ecosystems progresses, integrating these viral impacts in complex natural microbiome models will be key to accurately predict ecosystem biogeochemistry.

54 ENVIRONMENTAL SCIENCES↗

Five draft genome assemblies from Bacillaceae isolated from a degraded wetland environment

Abstract We isolated 5 Bacillaceae from a degraded wetland environment and sequenced their genomes using Illumina NextSeq. Here, we report draft genome sequences of Bacillus velezensus-SC119, Priestia megaterium-SC120, Bacillus zhangzhouensis-SC123, Bacillus pumilis-SC124, and Bacillus idriensis-SC127. The genomes range between 3,657,353 and 5,772,725 base pairs with %GC between 37.62% and 46.38%. Introduction Wetland environments play critical roles in the terrestrial carbon and water cycles and microbial communities are key players in healthy ecosystem function. Endospore forming bacteria in the Bacillaceae family are metabolically and genomically diverse soil heterotrophs that influence plant health, carbon and nitrogen cycling, and often produce diverse natural products that influence other bacterial and non-bacterial species in their environment (1). We collected two soil samples on January 19, 2023 from 42°43'12.7"N 73°45'01.4"W. One was highly hydrated and within a patch of invasive common reeds (Phragmites sp.) and the other was near the base of an Eastern cottonwood tree (Populus deltoides). Bacillus pumilis strain SC124 was isolated from the soil from near the cottonwood tree, while Bacillus velezensis strain SC119, Priestia megaterium strain SC120, Bacillus zhangzhouensis strain SC123, Bacillus idriensis strain SC127 and were isolated from the marshy soil.

isolate, wetlands, genome announcement↗