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East River Watershed hillslope‐riparian zone transect sampling sites. (a) The location of East River PLM intensive study site. (b) Five PLM sites are located across a hillslope transect. PLM0 is the highest point of the transect, and PLM4 is located in the floodplain. (c) Schematic representation of the sampling sites. Elevation of the surface, given in meters above sea level, appears below the name of the sampling site. Maximum depth at each sampling site is specified below the depiction of the sampled core in centimeters. Horizontal distances between sites are given at the bottom of the illustration. Maximum and minimum water levels are depicted by dashed blue and red lines, respectively. The PLM6 site was initially drilled for another study, 5 m from PLM3 but at the same elevation. A full view of the East River watershed is given in Figure A1
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Watersheds are important suppliers of freshwater for human societies. Within mountainous watersheds, microbial communities impact water chemistry and element fluxes as water from precipitation events discharge through soils and underlying weathered rock, yet there is limited information regarding the structure and function of these communities. Wit...
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Detailed descriptions of microbial communities have lagged far behind physical and chemical measurements in the marine environment. Here, we present 971 globally distributed surface ocean metagenomes collected at high spatio-temporal resolution. Our low-cost metagenomic sequencing protocol produced 3.65 terabases of data, where the median number of...
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Citations
... [30], but do not include the phyllosphere. Dodds et al. [31] studied the potential transfer of PMC's to waterways through run-off, but did not consider the role that waterways themselves have in influencing PMC's to begin with. ...
The role that aquatic aerosols might play in inter-ecosystem exchange in freshwater riparian environments has largely been understudied. In these environments, where freshwater streams are used both as drinking water and for treated waste disposal, water features like waterfalls, downed trees, and increased streamflow can serve as bioaerosol producers. Such water features could have an important role in the bacterial colonization of surrounding surfaces, including the riparian phyllosphere. In this study, we explore the influence of a freshwater stream’s bacterial community composition and micropollution on riparian maple leaves exposed to bioaerosols produced from the stream. Using culture-based and non-culture-based techniques, we compared phylloplane microbial communities in riparian zones, adjacent non-riparian forested zones, and the surface waters of the stream. In this system, riparian zone maple leaf surfaces had higher bacterial counts than non-riparian zone trees. Using metagenomic profiling of the 16S rRNA gene, we found that, while microbial communities on leaves in both riparian zone and forested sites were diverse, riparian zone bacterial communities were significantly more diverse. In addition, we found that riparian leaf bacterial communities shared more amplicon sequence variants (ASVs) with stream bacterial communities than forest leaves, indicating that the riparian zone phyllosphere is likely influenced by bioaerosols produced from water surfaces.
... However, microbial communities in weathered rocks-the precursors to soil-remain almost unstudied. Some exceptions include analysis of one metagenome of weathered shale [55] and two metagenomes in a weathered granodiorite [56]. In the current study, we analysed the metagenomes collected through a granite weathering profile. ...
... Proteins greater than 300 amino acids in length were retained and dereplicated at 95% similarity using CD-HIT resulting in 411 XoxF sequences. These sequences were concatenated with a reference set [16,55] and aligned using MAFFT using the following parameters: --localpair --maxiterate 1000 --reorder. The gaps were then removed from the alignments using trimal. ...
Background
Prior to soil formation, phosphate liberated by rock weathering is often sequestered into highly insoluble lanthanide phosphate minerals. Dissolution of these minerals releases phosphate and lanthanides to the biosphere. Currently, the microorganisms involved in phosphate mineral dissolution and the role of lanthanides in microbial metabolism are poorly understood.
Results
Although there have been many studies of soil microbiology, very little research has investigated microbiomes of weathered rock. Here, we sampled weathered granite and associated soil to identify the zones of lanthanide phosphate mineral solubilisation and genomically define the organisms implicated in lanthanide utilisation. We reconstructed 136 genomes from 11 bacterial phyla and found that gene clusters implicated in lanthanide-based metabolism of methanol (primarily xoxF3 and xoxF5) are surprisingly common in microbial communities in moderately weathered granite. Notably, xoxF3 systems were found in Verrucomicrobia for the first time, and in Acidobacteria, Gemmatimonadetes and Alphaproteobacteria. The xoxF-containing gene clusters are shared by diverse Acidobacteria and Gemmatimonadetes, and include conserved hypothetical proteins and transporters not associated with the few well studied xoxF systems. Given that siderophore-like molecules that strongly bind lanthanides may be required to solubilise lanthanide phosphates, it is notable that candidate metallophore biosynthesis systems were most prevalent in bacteria in moderately weathered rock, especially in Acidobacteria with lanthanide-based systems.
Conclusions
Phosphate mineral dissolution, putative metallophore production and lanthanide utilisation by enzymes involved in methanol oxidation linked to carbonic acid production co-occur in the zone of moderate granite weathering. In combination, these microbial processes likely accelerate the conversion of granitic rock to soil.
... Thus, despite the absence of sulfur respiration genes, CPRs can effectively participate in the sulfur cycle via hydrogenase-mediated sulfur reductase activity (Figure 1) [62]. Some other genomes have shown sulfur dioxygenase (sdo) and sulfate reduction genes (sat, cysC, and cysN) [63]. Through these processes, CPR organisms can play a vital role in nutrient cycling/secondary metabolism by breaking down complex organic molecules that other microorganisms are not capable of doing. ...
Microbial ecology is a critical field for understanding the composition, diversity, and functions of microorganisms in various environmental and health-related processes. The discovery of Candidate Phyla Radiation (CPR) through culture-independent methods has introduced a new division of microbes characterized by a symbiotic/parasitic lifestyle, small cell size, and small genome. Despite being poorly understood, CPRs have garnered significant attention in recent years due to their widespread detection in a variety of environmental and clinical samples. These microorganisms have been found to exhibit a high degree of genetic diversity compared to other microbes. Several studies have shed light on their potential importance in global biogeochemical cycles and their impact on various human activities. In this review, we provide a systematic overview of the discovery of CPRs. We then focus on describing how the genomic characteristics of CPRs have helped them interact with and adapt to other microbes in different ecological niches. Future works should focus on discovering the metabolic capacities of CPRs and, if possible, isolating them to obtain a better understanding of these microorganisms.
... However, we do note that removal of OC petro in the saturated zone is consistent with evidence for silicate mineral reactivity in the saturated zone based on stable lithium isotopes and reactive transport modeling (Golla et al., 2021(Golla et al., , 2022. Additionally, water saturated conditions promote different carbon degradation pathways (Lavy et al., 2019) that may favor OC petro as a carbon source, and the differing mechanical strength of organic matter within unweathered shales has been shown to promote exposure of OC petro through fracturing (Daigle et al., 2017). Therefore, we do not rule out the possibility of OC petro weathering at depths greater than the pyrite oxidation front. ...
... The presence of an active sulfur cycle was observed in the microbial data by Matheus Carnevali et al. (2021) who showed that genes encoding for S oxidation, including sulfide, sulfite, and thiosulfate oxidation, are prevalent in shallow floodplain soils (10-25 cm bgs) in the East River. Lavy et al. (2019) observed that saturated floodplain sediments in the East River supported an anaerobic microbial community, with a greater abundance of genes encoding for anaerobic carbon and nitrogen fixation and sulfur reduction, which was distinct from that in shallower unsaturated floodplain sediments and hillslope soils. Higher amounts of litter-derived organic matter and more oxic conditions in these shallow soil zones promote the biogeochemical cycling of sulfur, which is intricately linked with other nutrient cycles (e.g., carbon and nitrogen), through plant uptake, litter deposition and decomposition, and microbial processing. ...
Sulfur (S) is an essential macronutrient and important component of the earth’s crust, and its cycling has critical impacts on trace metal mobility, water quality, and human health. Pyrite weathering is the primary pathway by which sulfur enters surface waters. However, biogeochemical cycling of sulfur in soils and the river corridor mediates sulfate exports. In this study, we identified the major forms of sulfur across multiple compartments and scales in a pristine mountainous watershed, including shale bedrock weathering profiles, hillslope soils, and alluvial floodplain sediments, in order to provide insight into biogeochemical sulfur cycling in a hydrologically variable alpine system. X‐ray absorption near‐edge spectroscopy (XANES) analysis of shale weathering profiles showed clear evidence of pyrite oxidation to sulfate, with large accumulations of intermediate S(0) (20%–53%). Micro‐scale XANES showed evidence of reprecipitation of pyrite at fracture surfaces within the permanently saturated zone. Organic sulfur dominated S speciation in shallow hillslope soil and floodplain sediment, with little evidence of reduced inorganic S. However, mackinawite formation, representing active sulfate reduction, was observed in saturated oxbow sediments and saturated weathered shale underlying floodplain sediments. Further evidence of sulfate reduction from aqueous sulfur isotopic analysis was observed in shallow groundwater transects across an Fe‐reducing meander, whereas increases in pore water sulfate concentrations implied sulfur oxidation at other locations. The data present an integrated picture of sulfur cycling in a shale‐dominated watershed, where riverine sulfate exports are mediated by biological cycling, particularly in redox‐stratified and temporally dynamic hyporheic zone sediments.
... Soil microbial communities may be long-established and mineral weathering surfaces may be more depleted at some riparian sites based on disturbance history (e.g., Brantley et al. 2011;Lavy et al. 2019). Increases in dissolved nutrient concentrations likely increase immediately following disturbance and tree removal and recovery lasts more than 5 years. ...
Riparian zones are a vital interface between land and stream and are often the focus of stream restoration efforts to reduce nutrient pollution in waterways. Restoration of degraded stream channels often requires the removal of mature trees during major physical alteration of the riparian zone to reshape streambank topography. We assessed the impact of tree removal on riparian groundwater quality over space and time. Twenty-nine wells were installed across 5 sites in watersheds of the Washington D.C. and Baltimore, Maryland, USA metropolitan areas. Study sites encompassed a chronosequence of restoration ages (5, 10 and 20 years) as well as unrestored comparisons. Groundwater wells were installed as transects of 3 perpendicular to the stream channel to estimate nutrient uptake along groundwater flow paths. Groundwater samples collected over a 2-year period (2018-2019) were analyzed for concentrations of dissolved inorganic carbon (DIC), dissolved organic carbon (DOC), total dissolved nitrogen (TDN), and dissolved components of calcium (Ca), potassium (K), magnesium (Mg), sodium (Na), sulfur (S) and other elements. Results showed some interesting patterns such as: (1) elevated concentrations of some nutrients and carbon in riparian groundwater of recently restored (5 year) sites; (2) decreasing linear trends in concentrations of TDN, K and S in groundwater during a 2 year shift from wet to dry conditions; (3) linear relationships between DOC (organic matter) and plant nutrients in groundwater suggesting the importance of plant uptake and biomass as sources and sinks of nutrients; (4) increasing concentrations in groundwater along hydrologic flow paths from uplands to streams in riparian zones where trees were recently cut, and opposite patterns where trees were not cut. Riparian zones appeared to act as sources or sinks of bioreactive elements based on tree removal. Mean TDN, DOC, and S, concentrations decreased by 78.6%, 12.3%, and 19.3% respectively through uncut riparian zones, but increased by 516.9%, 199.7%, and 34.5% respectively through the 5-year cut transects. Ecosystem recovery and an improvement in groundwater quality appeared to be achieved by 10-20 years after restoration. A better understanding of the effects of riparian tree removal on groundwater quality can inform strategies for minimizing unintended effects of stream restoration on groundwater chemistry.
... Here we searched for additional genomes encoding related (divergent) amo/pmo's using a series of readily available, and custom built, hidden markov models (HMMs) across all archaeal genomes in the Genome Taxonomy Database (GTDB), and in all archaeal MAGs in our unpublished datasets from ongoing studies (Supplementary Fig. 1 and Supplementary Data 1). We found additional amoA/ pmoA genes in genomes recovered from soils at the South Meadow and Rivendell sites of the Angelo Coast Range Reserve (CA) [25,26], the nearby Sagehorn site [26], a hillslope of the East River watershed (CO) [27], and in sediments from the Rifle aquifer (CO) [28] and the deep ocean [29]. In total we identified 201 archaeal MAGs taxonomically placed using phylogenetically informative single copy marker genes outside of Nitrososphaerales containing divergent amo/pmo proteins (Supplementary Table 1 and Supplementary Data 1). ...
Copper membrane monooxygenases (CuMMOs) play critical roles in the global carbon and nitrogen cycles. Organisms harboring these enzymes perform the first, and rate limiting, step in aerobic oxidation of ammonia, methane, or other simple hydrocarbons. Within archaea, only organisms in the order Nitrososphaerales (Thaumarchaeota) encode CuMMOs, which function exclusively as ammonia monooxygenases. From grassland and hillslope soils and aquifer sediments, we identified 20 genomes from distinct archaeal species encoding divergent CuMMO sequences. These archaea are phylogenetically clustered in a previously unnamed Thermoplasmatota order, herein named the Ca. Angelarchaeales. The CuMMO proteins in Ca. Angelarchaeales are more similar in structure to those in Nitrososphaerales than those of bacteria, and contain all functional residues required for general monooxygenase activity. Ca. Angelarchaeales genomes are significantly enriched in blue copper proteins (BCPs) relative to sibling lineages, including plastocyanin-like electron carriers and divergent nitrite reductase-like ( nirK ) 2-domain cupredoxin proteins co-located with electron transport machinery. Ca. Angelarchaeales also encode significant capacity for peptide/amino acid uptake and degradation and share numerous electron transport mechanisms with the Nitrososphaerales. Ca. Angelarchaeales are detected at high relative abundance in some of the environments where their genomes originated from. While the exact substrate specificities of the novel CuMMOs identified here have yet to be determined, activity on ammonia is possible given their metabolic and ecological context. The identification of an archaeal CuMMO outside of the Nitrososphaerales significantly expands the known diversity of CuMMO enzymes in archaea and suggests previously unaccounted organisms contribute to critical global nitrogen and/or carbon cycling functions.
... However, CPR bacteria and DPANN archaea have rarely been studied in relatively oxic environments or identified in soil (1,9,10). Genome-resolved metagenomic analyses circumvent the limitations of isolation-based methods that fail for organisms unable to grow alone and for bacteria that evade detection by primers used in 16S rRNA gene surveys (11); yet, there are few reports of CPR metagenome-assembled genomes (MAGs) from soil (12)(13)(14)(15) almost certainly because of the rarity of these bacteria. ...
... Previously, a genome of TM7 (Saccharibacteria) was reported from the same soil but sampled at less than 1Â coverage from bulk soil (6), and Microgenomates and Parcubacteria have been genomically sampled at low abundance (13,23). To our knowledge, this is one of very few reports of Pacearchaeota and Doudnabacteria (14,15) in soil and the first report of a novel clade of Saccharibacteria. Comparing sequence coverage from concentrates to that from the bulk metagenomes, we calculate that filtration enriched the relative abundance of genomes by 100 to 1,000Â (Fig. 1c). ...
Here, we investigated overlooked microbes in soil, candidate phyla radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, by size fractionating small particles from soil, an approach typically used for the recovery of viral metagenomes. Concentration of these small cells (<0.2 μm) allowed us to identify these organisms as part of the rare soil biosphere and to sample genomes that were absent from non-size-fractionated metagenomes.
... Methods used for 2015 and 2016 metagenome assembly and annotation are described elsewhere [29]. In brief, after quality filtering, reads from individual samples were assembled separately using IDBA-UD v1.1.1 [30] with a minimum k-mer size of 40, a maximum k-mer size of 140, and step size of 20. ...
Background
Biogeochemical exports from watersheds are modulated by the activity of microorganisms that function over micron scales. Here, we tested the hypothesis that meander-bound regions share a core microbiome and exhibit patterns of metabolic potential that broadly predict biogeochemical processes in floodplain soils along a river corridor.
Results
We intensively sampled the microbiomes of floodplain soils located in the upper, middle, and lower reaches of the East River, Colorado. Despite the very high microbial diversity and complexity of the soils, we reconstructed 248 quality draft genomes representative of subspecies. Approximately one third of these bacterial subspecies was detected across all three locations at similar abundance levels, and ~ 15% of species were detected in two consecutive years. Within the meander-bound floodplains, we did not detect systematic patterns of gene abundance based on sampling position relative to the river. However, across meanders, we identified a core floodplain microbiome that is enriched in capacities for aerobic respiration, aerobic CO oxidation, and thiosulfate oxidation with the formation of elemental sulfur. Given this, we conducted a transcriptomic analysis of the middle floodplain. In contrast to predictions made based on the prominence of gene inventories, the most highly transcribed genes were relatively rare amoCAB and nxrAB (for nitrification) genes, followed by genes involved in methanol and formate oxidation, and nitrogen and CO2 fixation. Within all three meanders, low soil organic carbon correlated with high activity of genes involved in methanol, formate, sulfide, hydrogen, and ammonia oxidation, nitrite oxidoreduction, and nitrate and nitrite reduction. Overall, the results emphasize the importance of sulfur, one-carbon and nitrogen compound metabolism in soils of the riparian corridor.
Conclusions
The disparity between the scale of a microbial cell and the scale of a watershed currently limits the development of genomically informed predictive models describing watershed biogeochemical function. Meander-bound floodplains appear to serve as scaling motifs that predict aggregate capacities for biogeochemical transformations, providing a foundation for incorporating riparian soil microbiomes in watershed models. Widely represented genetic capacities did not predict in situ activity at one time point, but rather they define a reservoir of biogeochemical potential available as conditions change.
8muhHv3_-7zzU2wL3D8t9_Video abstract
... Here we searched for additional genomes encoding related (divergent) amo/pmos using a series of readily available, and custom built, hidden markov models (HMMs) across all archaeal genomes in the Genome Taxonomy Database (GTDB), and in all archaeal MAGs in our unpublished datasets from ongoing studies (Supplementary Fig. 1). We found additional amoA/pmoA genes in genomes recovered from soils at the South Meadow and Rivendell sites of the Angelo Coast Range Reserve (CA) 23,24 , the nearby Sagehorn site 24 , a hillslope of the East River watershed (CO) 25 , and in sediments from the Rifle aquifer (CO) 26 and the deep ocean 27 . In total we identified 201 archaeal MAGs taxonomically placed using phylogenetically informative single copy marker genes outside of Nitrososphaerales containing divergent amo/pmo proteins (Supplementary Table 1 and Supplementary Data 1). ...
Copper membrane monooxygenases (CuMMOs) play critical roles in the global carbon and nitrogen cycles. Organisms harboring these enzymes perform the first, and rate limiting, step in aerobic oxidation of ammonia, methane, or other simple hydrocarbons. Within archaea, only organisms in the order Nitrososphaerales (Thaumarchaeota) encode CuMMOs, which function exclusively as ammonia monooxygenases. From grassland and hillslope soils and aquifer sediments, we identified 20 genomes from distinct archaeal species encoding divergent CuMMO sequences. These archaea are phylogenetically clustered in a previously unnamed Thermoplasmatota order, herein named the Ca. Angelarcheales. The CuMMO proteins in Ca. Angelarcheales are more similar in structure to those in ammonia-oxidizing archaea than those of bacteria, and they contain all functional residues required for activity. Similarly to the Nitrososphaerales, Ca. Angelarcheales genomes are significantly enriched in blue copper proteins (BCPs) relative to sibling lineages, including plastocyanin-like electron carriers and divergent nitrite reductase-like (nirK) 2-domain cupredoxin proteins co-located with electron transport machinery. Angelarcheales do not have identifiable genes for methanol oxidation or carbon fixation, encode significant capacity for peptide/amino acid uptake and degradation, and share numerous electron transport mechanisms with the Nitrososphaerales. In the studied soils and sediments Ca. Angelarcheales were at least as abundant as ammonia-oxidizing Nitrososphaerales. Thus, we predict that Angelarcheales live a mixotrophic lifestyle based on oxidation of ammonia liberated from peptide and amino acid degradation. This work expands the known diversity of Thermoplasmatota and of CuMMO enzymes in archaea and suggests that these organisms are important and previously unaccounted for contributors to nitrogen cycling.
