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1. Assessment of Soil Features on the Growth of Environmental Nontuberculous Mycobacterial Isolates from Hawai'i

   https://doi.org/10.1128/AEM.00121-20  

   Glickman, Cody M. ; Virdi, Ravleen ; Hasan, Nabeeh A. ; Epperson, L. Elaine ; Brown, Leeza ; Dawrs, Stephanie N. ; Crooks, James L. ; Chan, Edward D. ; Strong, Michael ; Nelson, Stephen T. ; et al ( October 2020 , Applied and Environmental Microbiology)

   Alexandre, Gladys (Ed.)

   ABSTRACT Environmental nontuberculous mycobacteria (NTM), with the potential to cause opportunistic lung infections, can reside in soil. This might be particularly relevant in Hawai’i, a geographic hot spot for NTM infections and whose soil composition differs from many other areas of the world. Soil components are likely to contribute to NTM prevalence in certain niches as food sources or attachment scaffolds, but the particular types of soils, clays, and minerals that impact NTM growth are not well-defined. Hawai’i soil and chemically weathered rock (saprolite) samples were examined to characterize the microbiome and quantify 11 mineralogical features as well as soil pH. Machine learning methods were applied to identify important soil features influencing the presence of NTM. Next, these features were directly tested in vitro by incubating synthetic clays and minerals in the presence of Mycobacteroides abscessus and Mycobacterium chimaera isolates recovered from the Hawai'i environment, and changes in bacterial growth were determined. Of the components examined, synthetic gibbsite, a mineral form of aluminum hydroxide, inhibited the growth of both M. abscessus and M. chimaera , while other minerals tested showed differential effects on each species. For example, M. abscessus (but not M. chimaera ) growth was significantly higher in the presence of hematite, an iron oxide mineral. In contrast, M. chimaera (but not M. abscessus ) counts were significantly reduced in the presence of birnessite, a manganese-containing mineral. These studies shed new light on the mineralogic features that promote or inhibit the presence of Hawai’i NTM in Hawai’i soil. IMPORTANCE Globally and in the United States, the prevalence of NTM pulmonary disease—a potentially life-threatening but underdiagnosed chronic illness—is prominently rising. While NTM are ubiquitous in the environment, including in soil, the specific soil components that promote or inhibit NTM growth have not been elucidated. We hypothesized that NTM culture-positive soil contains minerals that promote NTM growth in vitro . Because Hawai’i is a hot spot for NTM and a unique geographic archipelago, we examined the composition of Hawai’i soil and identified individual clay, iron, and manganese minerals associated with NTM. Next, individual components were evaluated for their ability to directly modulate NTM growth in culture. In general, gibbsite and some manganese oxides were shown to decrease NTM, whereas iron-containing minerals were associated with higher NTM counts. These data provide new information to guide future analyses of soil-associated factors impacting persistence of these soil bacteria. 

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2. Phyllosphere Exudates Select for Distinct Microbiome Members in Sorghum Epicuticular Wax and Aerial Root Mucilage

   https://doi.org/10.1094/PBIOMES-08-22-0046-FI  

   Mechan-Llontop, Marco E. ; Mullet, John ; Shade, Ashley ( August 2023 , Phytobiomes Journal)

   Phyllosphere exudates create specialized microhabitats that shape microbial community diversity. We explored the microbiome associated with two sorghum phyllosphere exudates, the epicuticular wax and aerial root mucilage. We assessed the microbiome associated with the wax from sorghum plants over two growth stages, and the root mucilage additionally from nitrogen-fertilized and nonfertilized plants. In parallel, we isolated and characterized hundreds of bacteria from wax and mucilage, and integrated data from cultivation-independent and cultivation-dependent approaches to gain insights into exudate diversity and bacterial phenotypes. We found that Sphingomonadaceae and Rhizobiaceae families were the major taxa in the wax regardless of water availability and plant developmental stage to plants. The cultivation-independent mucilage-associated bacterial microbiome contained the families Erwiniaceae, Flavobacteriaceae, Rhizobiaceae, Pseudomonadaceae, and Sphingomonadaceae, and its structure was strongly influenced by sorghum development but only modestly influenced by fertilization. In contrast, the fungal community structure of mucilage was strongly affected by the year of sampling but not by fertilization or plant developmental stage, suggesting a decoupling of fungal–bacterial dynamics in the mucilage. Our bacterial isolate collection from wax and mucilage had several isolates that matched 100% to detected amplicon sequence variants, and were enriched on media that selected for phenotypes that included phosphate solubilization, putative diazotrophy, resistance to desiccation, capability to grow on methanol as a carbon source, and ability to grow in the presence of linalool and β-caryophyllene (terpenes in sorghum wax). This work expands our understanding of the microbiome of phyllosphere exudates and supports our long-term goal to translate microbiome research to support sorghum cultivation. 

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3. Long-Term Nutrient Enrichment of an Oligotroph-Dominated Wetland Increases Bacterial Diversity in Bulk Soils and Plant Rhizospheres

   https://doi.org/10.1128/mSphere.00035-20  

   Bledsoe, Regina B. ; Goodwillie, Carol ; Peralta, Ariane L. ( June 2020 , mSphere)

   Campbell, Barbara J. (Ed.)

   ABSTRACT In nutrient-limited conditions, plants rely on rhizosphere microbial members to facilitate nutrient acquisition, and in return, plants provide carbon resources to these root-associated microorganisms. However, atmospheric nutrient deposition can affect plant-microbe relationships by changing soil bacterial composition and by reducing cooperation between microbial taxa and plants. To examine how long-term nutrient addition shapes rhizosphere community composition, we compared traits associated with bacterial (fast-growing copiotrophs, slow-growing oligotrophs) and plant (C 3 forb, C 4 grass) communities residing in a nutrient-poor wetland ecosystem. Results revealed that oligotrophic taxa dominated soil bacterial communities and that fertilization increased the presence of oligotrophs in bulk and rhizosphere communities. Additionally, bacterial species diversity was greatest in fertilized soils, particularly in bulk soils. Nutrient enrichment (fertilized versus unfertilized) and plant association (bulk versus rhizosphere) determined bacterial community composition; bacterial community structure associated with plant functional group (grass versus forb) was similar within treatments but differed between fertilization treatments. The core forb microbiome consisted of 602 unique taxa, and the core grass microbiome consisted of 372 unique taxa. Forb rhizospheres were enriched in potentially disease-suppressive bacterial taxa, and grass rhizospheres were enriched in bacterial taxa associated with complex carbon decomposition. Results from this study demonstrate that fertilization serves as a strong environmental filter on the soil microbiome, which leads to distinct rhizosphere communities and can shift plant effects on the rhizosphere microbiome. These taxonomic shifts within plant rhizospheres could have implications for plant health and ecosystem functions associated with carbon and nitrogen cycling. IMPORTANCE Over the last century, humans have substantially altered nitrogen and phosphorus cycling. Use of synthetic fertilizer and burning of fossil fuels and biomass have increased nitrogen and phosphorus deposition, which results in unintended fertilization of historically low-nutrient ecosystems. With increased nutrient availability, plant biodiversity is expected to decline, and the abundance of copiotrophic taxa is anticipated to increase in bacterial communities. Here, we address how bacterial communities associated with different plant functional types (forb, grass) shift due to long-term nutrient enrichment. Unlike other studies, results revealed an increase in bacterial diversity, particularly of oligotrophic bacteria in fertilized plots. We observed that nutrient addition strongly determines forb and grass rhizosphere composition, which could indicate different metabolic preferences in the bacterial communities. This study highlights how long-term fertilization of oligotroph-dominated wetlands could alter diversity and metabolism of rhizosphere bacterial communities in unexpected ways. 

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4. Microbial community shifts in pearl millet root zone soils with Guiera senegalensis intercropping along a rainfall and soil type gradient in the Sahel

   https://doi.org/10.1002/saj2.20494  

   Mason, Laura ; Debenport, Spencer ; DeLay, Chelsea ; Diedhiou, Ibrahima ; McSpadden Gardener, Brian B. ; Assigbetsee, Komi B. ; Rich, Virginia ; Dick, Richard P. ( April 2023 , Soil Science Society of America Journal)

   The Sahel of West Africa has vulnerable agroecosystems that threatens food security. A potential solution is intercropping with the indigenous shrub,Guiera senegalensisJ.F. Gmel. Previous research of the Optimized Shrub‐intercropping System (OSS) (high density of ∼1,500 shrubs ha^‐1and coppiced residue incorporation) has been shown to dramatically improve pearl millet [Pennisetum glaucum(L.) R. Br.] yield, which is attributed to improved soil quality, nutrient and water availability, and harboring a distinct microbial community. Whether this response is consistent over a climate and soil type gradient in farmers’ fields has not been investigated. Therefore, the objective was to determine the impact ofG. senegalenison soil chemistry, enzyme activity, microbiomes, and metabolic pathways of millet root zone soils in farmers’ fields. The experiment was a three‐by‐two factorial with three rainfall and soil type sites along a north–south gradient in the Senegal Peanut Basin and two sampling locations (millet root zone soil within and outside the influence of theG. senegalensis).Guiera senegalensisshifted certain predicted bacterial metabolic pathways and enriched some bacterial and fungal genera. Notably, the increased crop growth due toG. senegalensispositively correlated with the abundance of genera having plant growth promoting properties (e.g.,Enterobacter agglomeransandParaburkholderia).Paucibacter, a genera that has deleterious and/or pathogenic properties, was highly abundant in non‐shrub soil but completely suppressed beneath the shrub. The results showed thatG. senegalensisin farmers’ fields even at typical, low densities, where coppiced residues are annually burned, still increased soil chemical and microbial properties, suggesting that a more important factor than litter is the presence of shrub roots that provide root turnover and exudates, and water inputs through hydraulic lift.

    

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5. Hyphae move matter and microbes to mineral microsites: Integrating the hyphosphere into conceptual models of soil organic matter stabilization

   https://doi.org/10.1111/gcb.16073  

   See, Craig R. ; Keller, Adrienne B. ; Hobbie, Sarah E. ; Kennedy, Peter G. ; Weber, Peter K. ; Pett‐Ridge, Jennifer ( January 2022 , Global Change Biology)

   Associations between soil minerals and microbially derived organic matter (often referred to as mineral‐associated organic matter or MAOM) form a large pool of slowly cycling carbon (C). The rhizosphere, soil immediately adjacent to roots, is thought to control the spatial extent of MAOM formation because it is the dominant entry point of new C inputs to soil. However, emphasis on the rhizosphere implicitly assumes that microbial redistribution of C into bulk (non‐rhizosphere) soils is minimal. We question this assumption, arguing that because of extensive fungal exploration and rapid hyphal turnover, fungal redistribution of soil C from the rhizosphere to bulk soil minerals is common, and encourages MAOM formation. First, we summarize published estimates of fungal hyphal length density and turnover rates and demonstrate that fungal C inputs are high throughout the rhizosphere–bulk soil continuum. Second, because colonization of hyphal surfaces is a common dispersal mechanism for soil bacteria, we argue that hyphal exploration allows for the non‐random colonization of mineral surfaces by hyphae‐associated taxa. Third, these bacterial communities and their fungal hosts determine the chemical form of organic matter deposited on colonized mineral surfaces. Collectively, our analysis demonstrates that omission of the hyphosphere from conceptual models of soil C flow overlooks key mechanisms for MAOM formation in bulk soils. Moving forward, there is a clear need for spatially explicit, quantitative research characterizing the environmental drivers of hyphal exploration and hyphosphere community composition across systems, as these are important controls over the rate and organic chemistry of C deposited on minerals.

    

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