A coupled microscopy approach to assess the nano-landscape of weathering

Mineral weathering is a balanced interplay among physical, chemical, and biological processes. Fundamental knowledge gaps exist in characterizing the biogeochemical mechanisms that transform microbe-mineral interfaces at submicron scales, particularly in complex field systems. Our objective was to develop methods targeting the nanoscale by using high-resolution microscopy to assess biological and geochemical drivers of weathering in natural settings. Basalt, granite, and quartz (53-250 mu m) were deployed in surface soils (10 cm) of three ecosystems (semiarid, subhumid, humid) for one year. We successfully developed a reference grid method to analyze individual grains using: (1) helium ion microscopy to capture micron to sub-nanometer imagery of mineral-organic interactions; and (2) scanning electron microscopy to quantify elemental distribution on the same surfaces via element mapping and point analyses. We detected locations of biomechanical weathering, secondary mineral precipitation, biofilm formation, and grain coatings across the three contrasting climates. To our knowledge, this is the first time these coupled microscopy techniques were applied in the earth and ecosystem sciences to assess microbe-mineral interfaces and in situ biological contributors to incipient weathering.Oregon State University faculty startup fund; Office of Biological and Environmental Research; NSF [EAR-GEO-1331846, EAR-0724958, IOS-1354219]; [EAR-1023215]Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons.

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

Continental-scale patterns of extracellular enzyme activity in the subsoil: an overlooked reservoir of microbial activity

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 &lt; 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. </div

Seed Banks, Seed Mortality, and the Role of Fungal Communities in Neotropical Forests

128 p.Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2007.Index words. Ascomycota; Cecropia; fungi; tropical forest ecology; seed bank; pioneer species; pathogens; ITS; Barro Colorado Island, Panama; La Selva, Costa Rica; Yasuni, Ecuador; recruitment limitation.U of I OnlyRestricted to the U of I community idenfinitely during batch ingest of legacy ETD

Seed Banks, Seed Mortality, and the Role of Fungal Communities in Neotropical Forests

128 p.Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2007.Index words. Ascomycota; Cecropia; fungi; tropical forest ecology; seed bank; pioneer species; pathogens; ITS; Barro Colorado Island, Panama; La Selva, Costa Rica; Yasuni, Ecuador; recruitment limitation.U of I OnlyRestricted to the U of I community idenfinitely during batch ingest of legacy ETD

Biochar and woodchip amendments alter restoration outcomes, microbial processes, and soil moisture in a simulated semi‐arid ecosystem

Amendments, such as woodchips or biochar, may improve success of arid and semi-arid wildland revegetation limited by unpredictable and insufficient rainfall as well as low soil water holding capacity. In an 116-day greenhouse experiment simulating a nearby savannah, response to four amendment treatments (no treatment, incorporated biochar, incorporated woodchips, and surface woodchips) was tested across two field soils (Chiricahua and Hathaway) and four simulated precipitation treatments (100, 80, 60, and 40% of average) in a replicated design. Soil type, amendment treatments, and simulated precipitation all had significant (p < 0.01) effects on aboveground biomass. The surface woodchip treatment averaged the highest biomass production of the amendment treatments (489 kg/ha) and the incorporated woodchips had the lowest (298 kg/ha). Aboveground biomass decreased with decreasing precipitation (533, 468, 350, and 216 kg/ha, respectively). Biochar amended soils averaged 5-10% higher volumetric water content than the woodchip amendments and controls through a 28-day dry down. Microbial nitrogen and phosphorus acquiring activities were higher in Hathaway soils while carbon activities were higher in Chiricahua soils. The surface woodchip treatment resulted in a different species composition than the other amendment and control treatments (p < 0.01). None of the amendment treatments ameliorated low precipitation conditions for plants. Contrary to expectations, carbon and phosphorus exoenzyme activities were highest in the lower precipitation treatments (60 and 40%) and nitrogen exoenzyme activities remained high in Hathaway soils regardless of precipitation. Surface application of woodchips increased vegetation as well as carbon and phosphorus exoenzyme activities while incorporating woodchips suppressed vegetation.12 month embargo; published online: 11 December 2019This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Soil amendments alter plant biomass and soil microbial activity in a semi-desert grassland

We tested the effects of soil biotic disturbance and biochar or woodchip amendments on plant growth, soil microbial biomass and activity, and soil physiochemical parameters in response to disturbance in a semi-desert grassland. In a 78-day growth chamber experiment using six grass species native to the Southwest U.S., we compared the effects of autoclave heatshock, which mimics soil stockpiling in hot drylands, and amendments on plant and microbial biomass, potential extracellular enzyme activity, and soil moisture and nutrient availability. Plant biomass was lowest in woodchip-amended soils, and highest in autoclaved and biochar-amended soils (p < 0.05). Root:shoot ratios were higher in the autoclaved and woodchip-amended soils (p < 0.05). Biochar addition improved soil water-holding capacity resulting in higher dissolved organic carbon (p < 0.001) and nitrogen (p < 0.001). Soil microbial activity and plant biomass were not correlated. Amendment-induced changes in activity could be partially explained by nutrient availability. Neither microbial biomass nor activity recovered to pre-disturbance values. In this study, biochar and woodchip amendment and autoclave-induced changes to moisture and nutrient availability influenced plant biomass allocation and soil microbial activity. Amendments increased carbon, nitrogen, and phosphorus mineralizing enzyme activities with no significant change in microbial biomass, indicating that soil recovery in drylands is a long-term process. Understanding plant-soil feedbacks in drylands is critically important to mitigating climate and anthropogenic-driven changes and retaining or reestablishing native plant communities.Rosemont Copper Company; University of Arizona Agricultural Experiment Station; National Institute of Food and Agriculture [NIFA ARZT-1360540-H12-199]12 month embargo; published online: 05 July 2017This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Appendix C. A table showing top BLAST matches (in GenBank) for ITS genotypes of fungi isolated from seeds of four Cecropia species following incubation for five months in the forest understory beneath four crowns of C. insignis.

A table showing top BLAST matches (in GenBank) for ITS genotypes of fungi isolated from seeds of four Cecropia species following incubation for five months in the forest understory beneath four crowns of C. insignis

Appendix A. A mixed-model ANOVA table showing fixed effects of seed species and burial location (crown) on seed survival and an ANOVA table showing effects of provenance, burial location, and maternal source on seed survival.

A mixed-model ANOVA table showing fixed effects of seed species and burial location (crown) on seed survival and an ANOVA table showing effects of provenance, burial location, and maternal source on seed survival