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  • 1
    In: Nature Microbiology, Springer Science and Business Media LLC, Vol. 9, No. 7 ( 2024-06-20), p. 1873-1883
    Abstract: Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities and interactions with the soil microbiome remains limited. Here we present the Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previously sequenced soil metagenomes and composed of 616,935 uncultivated viral genomes and 38,508 unique viral operational taxonomic units. Rarefaction curves from the Global Soil Virus Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared viral operational taxonomic units across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents an extensive characterization of soil viral diversity and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.
    Type of Medium: Online Resource
    ISSN: 2058-5276
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2024
    detail.hit.zdb_id: 2845610-5
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  • 2
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2021
    In:  ISME Communications Vol. 1, No. 1 ( 2021-12-01)
    In: ISME Communications, Oxford University Press (OUP), Vol. 1, No. 1 ( 2021-12-01)
    Abstract: Subsoil microbiomes play important roles in soil carbon and nutrient cycling, yet our understanding of the controls on subsoil microbial communities is limited. Here, we investigated the direct (mean annual temperature and precipitation) and indirect (soil chemistry) effects of climate on microbiome composition and extracellular enzyme activity throughout the soil profile across two elevation-bioclimatic gradients in central California, USA. We found that microbiome composition changes and activity decreases with depth. Across these sites, the direct influence of climate on microbiome composition and activity was relatively lower at depth. Furthermore, we found that certain microbial taxa change in relative abundance over large temperature and precipitation gradients only in specific soil horizons, highlighting the depth dependence of the climatic controls on microbiome composition. Our finding that the direct impacts of climate are muted at depth suggests that deep soil microbiomes may lag in their acclimation to new temperatures with a changing climate.
    Type of Medium: Online Resource
    ISSN: 2730-6151
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 3041786-7
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  • 3
    In: Ecological Applications, Wiley, Vol. 30, No. 4 ( 2020-06)
    Abstract: During the past century, systematic wildfire suppression has decreased fire frequency and increased fire severity in the western United States of America. While this has resulted in large ecological changes aboveground such as altered tree species composition and increased forest density, little is known about the long‐term, belowground implications of altered, ecologically novel, fire regimes, especially on soil biological processes. To better understand the long‐term implications of ecologically novel, high‐severity fire, we used a 44‐yr high‐severity fire chronosequence in the Sierra Nevada where forests were historically adapted to frequent, low‐severity fire, but were fire suppressed for at least 70 yr. High‐severity fire in the Sierra Nevada resulted in a long‐term (44 +yr) decrease ( 〉 50%, P   〈  0.05) in soil extracellular enzyme activities, basal microbial respiration (56–72%, P   〈  0.05), and organic carbon ( 〉 50%, P   〈  0.05) in the upper 5 cm compared to sites that had not been burned for at least 115 yr. However, nitrogen (N) processes were only affected in the most recent fire site (4 yr post‐fire). Net nitrification increased by over 600% in the most recent fire site ( P   〈  0.001), but returned to similar levels as the unburned control in the 13‐yr site. Contrary to previous studies, we did not find a consistent effect of plant cover type on soil biogeochemical processes in mid‐successional (10–50 yr) forest soils. Rather, the 44‐yr reduction in soil organic carbon (C) quantity correlated positively with dampened C cycling processes. Our results show the drastic and long‐term implication of ecologically novel, high‐severity fire on soil biogeochemistry and underscore the need for long‐term fire ecological experiments.
    Type of Medium: Online Resource
    ISSN: 1051-0761 , 1939-5582
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 1074505-1
    detail.hit.zdb_id: 2010123-5
    SSG: 12
    SSG: 23
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  • 4
    In: Environmental Research Letters, IOP Publishing, Vol. 15, No. 10 ( 2020-10-01), p. 1040a1-
    Abstract: Chemical stabilization of microbial-derived products such as extracellular enzymes (EE) onto mineral surfaces has gained attention as a possibly important mechanism leading to the persistence of soil organic carbon (SOC). While the controls on EE activities and their stabilization in the surface soil are reasonably well-understood, how these activities change with soil depth and possibly diverge from those at the soil surface due to distinct physical, chemical, and biotic conditions remains unclear. We assessed EE activity to a depth of 1 m (10 cm increments) in 19 soil profiles across the Critical Zone Observatory Network, which represents a wide range of climates, soil orders, and vegetation types. For all EEs, activities per mass of soil correlated positively with microbial biomass (MB) and SOC, and all three of these variables decreased logarithmically with depth ( p 〈 0.05). Across all sites, over half of the potential EE activities per mass soil consistently occurred below 20 cm for all measured EEs. Activities per unit MB or SOC were substantially higher at depth (soils below 20 cm accounted for 80% of whole-profile EE activity), suggesting an accumulation of stabilized (i.e. mineral sorbed) EEs in subsoil horizons. The pronounced enzyme stabilization in subsurface horizons was corroborated by mixed-effects models that showed a significant, positive relationship between clay concentration and MB-normalized EE activities in the subsoil. Furthermore, the negative relationships between soil C, N, and P and C-, N-, and P-acquiring EEs found in the surface soil decoupled below 20 cm, which could have also been caused by EE stabilization. This finding suggests that EEs may not reflect soil nutrient availabilities deeper in the soil profile. Taken together, our results suggest that deeper soil horizons hold a significant reservoir of EEs, and that the controls of subsoil EEs differ from their surface soil counterparts.
    Type of Medium: Online Resource
    ISSN: 1748-9326
    Language: Unknown
    Publisher: IOP Publishing
    Publication Date: 2020
    detail.hit.zdb_id: 2255379-4
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  • 5
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2022
    In:  The ISME Journal Vol. 16, No. 7 ( 2022-07-01), p. 1853-1863
    In: The ISME Journal, Oxford University Press (OUP), Vol. 16, No. 7 ( 2022-07-01), p. 1853-1863
    Abstract: Increasing wildfire severity, which is common throughout the western United States, can have deleterious effects on plant regeneration and large impacts on carbon (C) and nitrogen (N) cycling rates. Soil microbes are pivotal in facilitating these elemental cycles, so understanding the impact of increasing fire severity on soil microbial communities is critical. Here, we assess the long-term impact of high-severity fires on the soil microbiome. We find that high-severity wildfires result in a multi-decadal ( & gt;25 y) recovery of the soil microbiome mediated by concomitant differences in aboveground vegetation, soil chemistry, and microbial assembly processes. Our results depict a distinct taxonomic and functional successional pattern of increasing selection in post-fire soil microbial communities. Changes in microbiome composition corresponded with changes in microbial functional potential, specifically altered C metabolism and enhanced N cycling potential, which related to rates of potential decomposition and inorganic N availability, respectively. Based on metagenome-assembled genomes, we show that bacterial genomes enriched in our earliest site (4 y since fire) harbor distinct traits such as a robust stress response and a high potential to degrade pyrogenic, polyaromatic C that allow them to thrive in post-fire environments. Taken together, these results provide a biological basis for previously reported process rate measurements and explain the temporal dynamics of post-fire biogeochemistry, which ultimately constrains ecosystem recovery.
    Type of Medium: Online Resource
    ISSN: 1751-7362 , 1751-7370
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2299378-2
    detail.hit.zdb_id: 2406536-5
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  • 6
    In: mBio, American Society for Microbiology, Vol. 10, No. 5 ( 2019-10-29)
    Abstract: While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi , Nitrospirae , Euryarchaeota , and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments. IMPORTANCE Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions.
    Type of Medium: Online Resource
    ISSN: 2161-2129 , 2150-7511
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2019
    detail.hit.zdb_id: 2557172-2
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  • 7
    In: Ecology, Wiley, Vol. 100, No. 7 ( 2019-07)
    Abstract: Understanding how altered soil organic carbon ( SOC ) availability affects microbial communities and their function is imperative in predicting impacts of global change on soil carbon (C) storage and ecosystem function. However, the response of soil microbial communities and their function to depleted C availability in situ is unclear. We evaluated the role of soil C inputs in controlling microbial biomass, community composition, physiology, and function by (1) experimentally excluding plant C inputs in situ for 9 yr in four temperate forest ecosystems along a productivity gradient in Oregon, USA ; and (2) integrating these findings with published data from similar C‐exclusion studies into a global meta‐analysis. Excluding plant C inputs for 9 yr resulted in a 13% decrease in SOC across the four Oregon sites and an overall shift in the microbial community composition, with a 45% decrease in the fungal : bacterial ratio and a 13% increase in Gram‐positive : Gram‐negative bacterial ratio. Although gross N mineralization decreased under C exclusion, decreases in gross N immobilization were greater, resulting in increased net N mineralization rates in all but the lowest‐productivity site. Microbial biomass showed a variable response to C exclusion that was method dependent; however, we detected a 29% decrease in C‐use efficiency across the sites, with greater declines occurring in less‐productive sites. Although extracellular enzyme activity increased with C exclusion, C exclusion resulted in a 31% decrease in microbial respiration across all sites. Our meta‐analyses of published data with similar C‐exclusion treatments were largely consistent with our experimental results, showing decreased SOC , fungal : bacterial ratios, and microbial respiration, and increased Gram‐positive : Gram‐negative bacterial ratio following exclusion of C inputs to soil. Effect sizes of SOC and respiration correlated negatively with the duration of C exclusion; however, there were immediate effects of C exclusion on microbial community composition and biomass that were unaltered by duration of treatment. Our field‐based experimental results and analyses demonstrate unequivocally the dominant control of C availability on soil microbial biomass, community composition, and function, and provide additional insight into the mechanisms for these effects in forest ecosystems.
    Type of Medium: Online Resource
    ISSN: 0012-9658 , 1939-9170
    URL: Issue
    RVK:
    Language: English
    Publisher: Wiley
    Publication Date: 2019
    detail.hit.zdb_id: 1797-8
    detail.hit.zdb_id: 2010140-5
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2021
    In:  Nature Communications Vol. 12, No. 1 ( 2021-04-07)
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 12, No. 1 ( 2021-04-07)
    Abstract: Increasing global temperatures are predicted to stimulate soil microbial respiration. The direct and indirect impacts of warming on soil microbes, nevertheless, remain unclear. This is particularly true for understudied subsoil microbes. Here, we show that 4.5 years of whole-profile soil warming in a temperate mixed forest results in altered microbial community composition and metabolism in surface soils, partly due to carbon limitation. However, microbial communities in the subsoil responded differently to warming than in the surface. Throughout the soil profile—but to a greater extent in the subsoil—physiologic and genomic measurements show that phylogenetically different microbes could utilize complex organic compounds, dampening the effect of altered resource availability induced by warming. We find subsoil microbes had 20% lower carbon use efficiencies and 47% lower growth rates compared to surface soils, which constrain microbial communities. Collectively, our results show that unlike in surface soils, elevated microbial respiration in subsoils may continue without microbial community change in the near-term.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2553671-0
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  • 9
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2022
    In:  Journal of Applied Microbiology Vol. 133, No. 6 ( 2022-12-01), p. 3768-3776
    In: Journal of Applied Microbiology, Oxford University Press (OUP), Vol. 133, No. 6 ( 2022-12-01), p. 3768-3776
    Abstract: We compared the bacterial endophytic communities of three genetically different almond cultivars that were all grafted on the same type of rootstock, growing side by side within a commercial orchard. Methods and Results We examined the diversity of leaf bacterial endophytes using cultivation-independent techniques and assessed the relative abundance of bacterial families. Two of these three cultivars were dominated by Pseudomonadaceae, while the bacterial composition of the third cultivar consisted mainly of Streptococcaceae. Conclusions The experimental set up allowed us to analyse the impact of the shoot cultivar on endophytes, minimizing the influence of rootstock, biogeography, and cultivation status. Our data suggest that the shoot cultivar can shape the leaf endophytic community composition of almond trees. Significance and Impact of the Study Our results suggest that the shoot cultivar controls the composition of the foliar bacterial endophytic community of almonds. Overall, our results could provide a first step to develop strategies for a more sustainable almond agriculture.
    Type of Medium: Online Resource
    ISSN: 1365-2672 , 1364-5072
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2020421-8
    detail.hit.zdb_id: 1358023-1
    SSG: 12
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  • 10
    In: Soil Biology and Biochemistry, Elsevier BV, Vol. 99 ( 2016-08), p. 158-166
    Type of Medium: Online Resource
    ISSN: 0038-0717
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2016
    detail.hit.zdb_id: 280810-9
    SSG: 12
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