1
|
Kakouridis A, Yuan M, Nuccio EE, Hagen JA, Fossum CA, Moore ML, Estera-Molina KY, Nico PS, Weber PK, Pett-Ridge J, Firestone MK. Arbuscular mycorrhiza convey significant plant carbon to a diverse hyphosphere microbial food web and mineral-associated organic matter. New Phytol 2024; 242:1661-1675. [PMID: 38358052 DOI: 10.1111/nph.19560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 12/04/2023] [Indexed: 02/16/2024]
Abstract
Arbuscular mycorrhizal fungi (AMF) transport substantial plant carbon (C) that serves as a substrate for soil organisms, a precursor of soil organic matter (SOM), and a driver of soil microbial dynamics. Using two-chamber microcosms where an air gap isolated AMF from roots, we 13CO2-labeled Avena barbata for 6 wk and measured the C Rhizophagus intraradices transferred to SOM and hyphosphere microorganisms. NanoSIMS imaging revealed hyphae and roots had similar 13C enrichment. SOM density fractionation, 13C NMR, and IRMS showed AMF transferred 0.77 mg C g-1 of soil (increasing total C by 2% relative to non-mycorrhizal controls); 33% was found in occluded or mineral-associated pools. In the AMF hyphosphere, there was no overall change in community diversity but 36 bacterial ASVs significantly changed in relative abundance. With stable isotope probing (SIP)-enabled shotgun sequencing, we found taxa from the Solibacterales, Sphingobacteriales, Myxococcales, and Nitrososphaerales (ammonium oxidizing archaea) were highly enriched in AMF-imported 13C (> 20 atom%). Mapping sequences from 13C-SIP metagenomes to total ASVs showed at least 92 bacteria and archaea were significantly 13C-enriched. Our results illustrate the quantitative and ecological impact of hyphal C transport on the formation of potentially protective SOM pools and microbial roles in the AMF hyphosphere soil food web.
Collapse
Affiliation(s)
- Anne Kakouridis
- University of California Berkeley, Berkeley, CA, 94720, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mengting Yuan
- University of California Berkeley, Berkeley, CA, 94720, USA
| | - Erin E Nuccio
- Lawrence Livermore National Laboratory, Livermore, 94550, CA, USA
| | - John A Hagen
- University of California Berkeley, Berkeley, CA, 94720, USA
| | | | - Madeline L Moore
- University of California Berkeley, Berkeley, CA, 94720, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Katerina Y Estera-Molina
- University of California Berkeley, Berkeley, CA, 94720, USA
- Lawrence Livermore National Laboratory, Livermore, 94550, CA, USA
| | - Peter S Nico
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Peter K Weber
- Lawrence Livermore National Laboratory, Livermore, 94550, CA, USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Livermore, 94550, CA, USA
- University of California Merced, Merced, 95343, CA, USA
| | | |
Collapse
|
2
|
Nuccio EE, Blazewicz SJ, Lafler M, Campbell AN, Kakouridis A, Kimbrel JA, Wollard J, Vyshenska D, Riley R, Tomatsu A, Hestrin R, Malmstrom RR, Firestone M, Pett-Ridge J. HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi. Microbiome 2022; 10:199. [PMID: 36434737 PMCID: PMC9700909 DOI: 10.1186/s40168-022-01391-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Linking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists. Of many techniques that strive for this goal, Stable-isotope probing-SIP-remains among the most comprehensive for studying whole microbial communities in situ. In DNA-SIP, actively growing microorganisms that take up an isotopically heavy substrate build heavier DNA, which can be partitioned by density into multiple fractions and sequenced. However, SIP is relatively low throughput and requires significant hands-on labor. We designed and tested a semi-automated, high-throughput SIP (HT-SIP) pipeline to support well-replicated, temporally resolved amplicon and metagenomics experiments. We applied this pipeline to a soil microhabitat with significant ecological importance-the hyphosphere zone surrounding arbuscular mycorrhizal fungal (AMF) hyphae. AMF form symbiotic relationships with most plant species and play key roles in terrestrial nutrient and carbon cycling. RESULTS Our HT-SIP pipeline for fractionation, cleanup, and nucleic acid quantification of density gradients requires one-sixth of the hands-on labor compared to manual SIP and allows 16 samples to be processed simultaneously. Automated density fractionation increased the reproducibility of SIP gradients compared to manual fractionation, and we show adding a non-ionic detergent to the gradient buffer improved SIP DNA recovery. We applied HT-SIP to 13C-AMF hyphosphere DNA from a 13CO2 plant labeling study and created metagenome-assembled genomes (MAGs) using high-resolution SIP metagenomics (14 metagenomes per gradient). SIP confirmed the AMF Rhizophagus intraradices and associated MAGs were highly enriched (10-33 atom% 13C), even though the soils' overall enrichment was low (1.8 atom% 13C). We assembled 212 13C-hyphosphere MAGs; the hyphosphere taxa that assimilated the most AMF-derived 13C were from the phyla Myxococcota, Fibrobacterota, Verrucomicrobiota, and the ammonia-oxidizing archaeon genus Nitrososphaera. CONCLUSIONS Our semi-automated HT-SIP approach decreases operator time and improves reproducibility by targeting the most labor-intensive steps of SIP-fraction collection and cleanup. We illustrate this approach in a unique and understudied soil microhabitat-generating MAGs of actively growing microbes living in the AMF hyphosphere (without plant roots). The MAGs' phylogenetic composition and gene content suggest predation, decomposition, and ammonia oxidation may be key processes in hyphosphere nutrient cycling. Video Abstract.
Collapse
Affiliation(s)
- Erin E. Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Steven J. Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Marissa Lafler
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Ashley N. Campbell
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Anne Kakouridis
- Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
- Department of Environmental Science Policy and Management, University of California, Berkeley, CA USA
| | - Jeffrey A. Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Jessica Wollard
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | | | | | | | - Rachel Hestrin
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA USA
| | | | - Mary Firestone
- Department of Environmental Science Policy and Management, University of California, Berkeley, CA USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
- Life & Environmental Sciences Department, University of California Merced, Merced, CA USA
| |
Collapse
|
3
|
Kakouridis A, Hagen JA, Kan MP, Mambelli S, Feldman LJ, Herman DJ, Weber PK, Pett‐Ridge J, Firestone MK. Routes to roots: direct evidence of water transport by arbuscular mycorrhizal fungi to host plants. New Phytol 2022; 236:210-221. [PMID: 35633108 PMCID: PMC9543596 DOI: 10.1111/nph.18281] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/16/2022] [Indexed: 05/19/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) can help mitigate plant responses to water stress, but it is unclear whether AMF do so by indirect mechanisms, direct water transport to roots, or a combination of the two. Here, we investigated if and how the AMF Rhizophagus intraradices transported water to the host plant Avena barbata, wild oat. We used two-compartment microcosms, isotopically labeled water, and a fluorescent dye to directly track and quantify water transport by AMF across an air gap to host plants. Plants grown with AMF that had access to a physically separated compartment containing 18 O-labeled water transpired almost twice as much as plants with AMF excluded from that compartment. Using an isotopic mixing model, we estimated that water transported by AMF across the air gap accounted for 34.6% of the water transpired by host plants. In addition, a fluorescent dye indicated that hyphae were able to transport some water via an extracytoplasmic pathway. Our study provides direct evidence that AMF can act as extensions of the root system along the soil-plant-air continuum of water movement, with plant transpiration driving water flow along hyphae outside of the hyphal cell membrane.
Collapse
Affiliation(s)
- Anne Kakouridis
- University of California BerkeleyBerkeleyCA94720USA
- Lawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | | | - Megan P. Kan
- University of California BerkeleyBerkeleyCA94720USA
- Lawrence Livermore National LaboratoryLivermoreCA94550USA
| | - Stefania Mambelli
- University of California BerkeleyBerkeleyCA94720USA
- Center for Stable Isotope BiogeochemistryBerkeleyCA94720USA
| | | | - Donald J. Herman
- University of California BerkeleyBerkeleyCA94720USA
- Lawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Peter K. Weber
- Lawrence Livermore National LaboratoryLivermoreCA94550USA
| | - Jennifer Pett‐Ridge
- Lawrence Livermore National LaboratoryLivermoreCA94550USA
- University of California MercedMercedCA95344USA
| | | |
Collapse
|
4
|
Matzen SL, Lobo GP, Fakra SC, Kakouridis A, Nico PS, Pallud CE. Arsenic hyperaccumulator Pteris vittata shows reduced biomass in soils with high arsenic and low nutrient availability, leading to increased arsenic leaching from soil. Sci Total Environ 2022; 818:151803. [PMID: 34808151 DOI: 10.1016/j.scitotenv.2021.151803] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/06/2021] [Accepted: 11/15/2021] [Indexed: 06/13/2023]
Abstract
Plant-soil interactions affect arsenic and nutrient availability in arsenic-contaminated soils, with implications for arsenic uptake and tolerance in plants, and leaching from soil. In 22-week column experiments, we grew the arsenic hyperaccumulating fern Pteris vittata in a coarse- and a medium-textured soil to determine the effects of phosphorus fertilization and mycorrhizal fungi inoculation on P. vittata arsenic uptake and arsenic leaching. We investigated soil arsenic speciation using synchrotron-based spectromicroscopy. Greater soil arsenic availability and lower nutrient content in the coarse-textured soil were associated with greater fern arsenic uptake, lower biomass (apparently a metabolic cost of tolerance), and arsenic leaching from soil, due to lower transpiration. P. vittata hyperaccumulated arsenic from coarse- but not medium-textured soil. Mass of plant-accumulated arsenic was 1.2 to 2.4 times greater, but aboveground biomass was 74% smaller, in ferns growing in coarse-textured soil. In the presence of ferns, mean arsenic loss by leaching was 195% greater from coarse- compared to the medium-textured soil, and lower across both soils compared to the absence of ferns. In the medium-textured soil arsenic concentrations in leachate were higher in the presence of ferns. Fern arsenic uptake was always greater than loss by leaching. Most arsenic (>66%) accumulated in P. vittata appeared of rhizosphere origin. In the medium-textured soil with more clay and higher nutrient content, successful iron scavenging increased arsenic release from soil for leaching, but transpiration curtailed leaching.
Collapse
Affiliation(s)
- S L Matzen
- Department of Environmental Science, Policy, and Management, University of California-Berkeley, 130 Mulford Hall, Berkeley, CA 94720, USA
| | - G P Lobo
- Civil and Environmental Engineering, University of California-Berkeley, 410 O'Brien Hall, Berkeley, CA 94720, USA
| | - S C Fakra
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - A Kakouridis
- Department of Environmental Science, Policy, and Management, University of California-Berkeley, 130 Mulford Hall, Berkeley, CA 94720, USA
| | - P S Nico
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - C E Pallud
- Department of Environmental Science, Policy, and Management, University of California-Berkeley, 130 Mulford Hall, Berkeley, CA 94720, USA.
| |
Collapse
|
5
|
Guzman A, Montes M, Hutchins L, DeLaCerda G, Yang P, Kakouridis A, Dahlquist‐Willard RM, Firestone MK, Bowles T, Kremen C. Crop diversity enriches arbuscular mycorrhizal fungal communities in an intensive agricultural landscape. New Phytol 2021; 231:447-459. [PMID: 33638170 PMCID: PMC9292320 DOI: 10.1111/nph.17306] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 02/08/2021] [Accepted: 02/15/2021] [Indexed: 05/21/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are keystone symbionts of agricultural soils but agricultural intensification has negatively impacted AMF communities. Increasing crop diversity could ameliorate some of these impacts by positively affecting AMF. However, the underlying relationship between plant diversity and AMF community composition has not been fully resolved. We examined how greater crop diversity affected AMF across farms in an intensive agricultural landscape, defined by high nutrient input, low crop diversity and high tillage frequency. We assessed AMF communities across 31 field sites that were either monocultures or polycultures (growing > 20 different crop types) in three ways: richness, diversity and composition. We also determined root colonization across these sites. We found that polycultures drive the available AMF community into richer and more diverse communities while soil properties structure AMF community composition. AMF root colonization did not vary by farm management (monocultures vs polycultures), but did vary by crop host. We demonstrate that crop diversity enriches AMF communities, counteracting the negative effects of agricultural intensification on AMF, providing the potential to increase agroecosystem functioning and sustainability.
Collapse
Affiliation(s)
- Aidee Guzman
- Department of Environmental Science, Policy, and ManagementUniversity of California, BerkeleyBerkeleyCA94720USA
| | - Marisol Montes
- Department of Environmental Science, Policy, and ManagementUniversity of California, BerkeleyBerkeleyCA94720USA
| | - Leslie Hutchins
- Department of Environmental Science, Policy, and ManagementUniversity of California, BerkeleyBerkeleyCA94720USA
| | - Gisel DeLaCerda
- Department of Environmental Science, Policy, and ManagementUniversity of California, BerkeleyBerkeleyCA94720USA
| | - Paula Yang
- Department of BiologyCalifornia State University, FresnoFresnoCA93740USA
| | - Anne Kakouridis
- Department of Environmental Science, Policy, and ManagementUniversity of California, BerkeleyBerkeleyCA94720USA
| | | | - Mary K. Firestone
- Department of Environmental Science, Policy, and ManagementUniversity of California, BerkeleyBerkeleyCA94720USA
| | - Timothy Bowles
- Department of Environmental Science, Policy, and ManagementUniversity of California, BerkeleyBerkeleyCA94720USA
| | - Claire Kremen
- Department of Environmental Science, Policy, and ManagementUniversity of California, BerkeleyBerkeleyCA94720USA
- Institute for Resources, Environment and SustainabilityUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
| |
Collapse
|
6
|
Yuan MM, Kakouridis A, Starr E, Nguyen N, Shi S, Pett-Ridge J, Nuccio E, Zhou J, Firestone M. Fungal-Bacterial Cooccurrence Patterns Differ between Arbuscular Mycorrhizal Fungi and Nonmycorrhizal Fungi across Soil Niches. mBio 2021; 12:e03509-20. [PMID: 33879589 PMCID: PMC8092305 DOI: 10.1128/mbio.03509-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/04/2021] [Indexed: 11/20/2022] Open
Abstract
Soil bacteria and fungi are known to form niche-specific communities that differ between actively growing and decaying roots. Yet almost nothing is known about the cross-kingdom interactions that frame these communities and the environmental filtering that defines these potentially friendly or competing neighbors. We explored the temporal and spatial patterns of soil fungal (mycorrhizal and nonmycorrhizal) and bacterial cooccurrence near roots of wild oat grass, Avena fatua, growing in its naturalized soil in a greenhouse experiment. Amplicon sequences of the fungal internal transcribed spacer (ITS) and bacterial 16S rRNA genes from rhizosphere and bulk soils collected at multiple plant growth stages were used to construct covariation-based networks as a step toward identifying fungal-bacterial associations. Corresponding stable-isotope-enabled metagenome-assembled genomes (MAGs) of bacteria identified in cooccurrence networks were used to inform potential mechanisms underlying the observed links. Bacterial-fungal networks were significantly different in rhizosphere versus bulk soils and between arbuscular mycorrhizal fungi (AMF) and nonmycorrhizal fungi. Over 12 weeks of plant growth, nonmycorrhizal fungi formed increasingly complex networks with bacteria in rhizosphere soils, while AMF more frequently formed networks with bacteria in bulk soils. Analysis of network-associated bacterial MAGs suggests that some of the fungal-bacterial links that we identified are potential indicators of bacterial breakdown and consumption of fungal biomass, while others intimate shared ecological niches.IMPORTANCE Soils near living and decomposing roots form distinct niches that promote microorganisms with distinctive environmental preferences and interactions. Yet few studies have assessed the community-level cooccurrence of bacteria and fungi in these soil niches as plant roots grow and senesce. With plant growth, we observed increasingly complex cooccurrence networks between nonmycorrhizal fungi and bacteria in the rhizosphere, while mycorrhizal fungal (AMF) and bacterial cooccurrence was more pronounced in soil further from roots, in the presence of decaying root litter. This rarely documented phenomenon suggests niche sharing of nonmycorrhizal fungi and bacteria, versus niche partitioning between AMF and bacteria; both patterns are likely driven by C substrate availability and quality. Although the implications of species cooccurrence are fiercely debated, MAGs matching the bacterial nodes in our networks possess the functional potential to interact with the fungi that they are linked to, suggesting an ecological significance of fungal-bacterial cooccurrence patterns.
Collapse
Affiliation(s)
- Mengting Maggie Yuan
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, USA
| | - Anne Kakouridis
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, USA
| | - Evan Starr
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Nhu Nguyen
- Department of Tropical Plants and Soil Sciences, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Shengjing Shi
- AgResearch Ltd., Lincoln Science Centre, Christchurch, New Zealand
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Erin Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Mary Firestone
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| |
Collapse
|