The biodiversity of microbial communities has important implications for the stability and functioning of ecosystem processes. Yet, very little is known about the environmental factors that define the microbial niche and how this influences the composition and activity of microbial communities. In this study, we derived niche parameters from physiological response curves that quantified microbial respiration for a diverse collection of soil bacteria and fungi along a soil moisture gradient. On average, soil microorganisms had relatively dry optima (0.3 MPa) and were capable of respiring under low water potentials (−2.0 MPa). Within their limits of activity, microorganisms exhibited a wide range of responses, suggesting that some taxa may be able to coexist by partitioning the moisture niche axis. For example, we identified dry‐adapted generalists that tolerated a broad range of water potentials, along with wet‐adapted specialists with metabolism restricted to less‐negative water potentials. These contrasting ecological strategies had a phylogenetic signal at a coarse taxonomic level (phylum), suggesting that the moisture niche of soil microorganisms is highly conserved. In addition, variation in microbial responses along the moisture gradient was linked to the distribution of several functional traits. In particular, strains that were capable of producing biofilms had drier moisture optima and wider niche breadths. However, biofilm production appeared to come at a cost that was reflected in a prolonged lag time prior to exponential growth, suggesting that there is a trade‐off associated with traits that allow microorganisms to contend with moisture stress. Together, we have identified functional groups of microorganisms that will help predict the structure and functioning of microbial communities under contrasting soil moisture regimes.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the coronavirus disease (COVID-19), is shed in feces and the viral ribonucleic acid (RNA) is detectable in wastewater. A nine-week wastewater epidemiology study of ten wastewater facilities, serving 39% of the state of Utah or 1.26 M individuals was conducted in April and May of 2020. COVID-19 cases were tabulated from within each sewershed boundary. RNA from SARS-CoV-2 was detectable in 61% of 126 wastewater samples. Urban sewersheds serving >100,000 individuals and tourist communities had higher detection frequencies. An outbreak of COVID-19 across two communities positively correlated with an increase in wastewater SARS-CoV-2 RNA, while a decline in COVID-19 cases preceded a decline in RNA. SARS-CoV-2 RNA followed a first order decay rate in wastewater, while 90% of the RNA was present in the liquid phase of the influent. Infiltration and inflow, virus decay and sewershed characteristics should be considered during correlation analysis of SAR-CoV-2 with COVID-19 cases. These results provide evidence of the utility of wastewater epidemiology to assist in public health responses to COVID-19.

Dormancy is a life history trait that may have important implications for linking microbial communities to the functioning of natural and managed ecosystems. Rapid changes in environmental cues may resuscitate dormant bacteria and create pulses of ecosystem activity. In this study, we used heavy-water (H182O) stable isotope probing (SIP) to identify fast-growing bacteria that were associated with pulses of trace gasses (CO2, CH4, and N2O) from different ecosystems [agricultural site, grassland, deciduous forest, and coniferous forest (CF)] following a soil-rewetting event. Irrespective of ecosystem type, a large fraction (69–74%) of the bacteria that responded to rewetting were below detection limits in the dry soils. Based on the recovery of sequences, in just a few days, hundreds of rare taxa increased in abundance and in some cases became dominant members of the rewetted communities, especially bacteria belonging to the Sphingomonadaceae, Comamonadaceae, and Oxalobacteraceae. Resuscitation led to dynamic shifts in the rank abundance of taxa that caused previously rare bacteria to comprise nearly 60% of the sequences that were recovered in rewetted communities. This rapid turnover of the bacterial community corresponded with a 5–20-fold increase in the net production of CO2 and up to a 150% reduction in the net production of CH4 from rewetted soils. Results from our study demonstrate that the rare biosphere may account for a large and dynamic fraction of a community that is important for the maintenance of bacterial biodiversity. Moreover, our findings suggest that the resuscitation of rare taxa from seed banks contribute to ecosystem functioning.

Resource partitioning has been suggested as an important mechanism of invasion resistance. The relative importance of resource partitioning for invasion resistance, however, may depend on how species abundance is distributed in the plant community. This study had two objectives. First, we quantified the degree to which one resource, nitrogen (N), is partitioned by time, depth and chemical form among coexisting species from different functional groups by injecting (15)N into soils around the study species three times during the growing season, at two soil depths and as two chemical forms. A watering treatment also was applied to evaluate the impact of soil water content on N partitioning. Second, we examined the degree to which native functional groups contributed to invasion resistance by seeding a non-native annual grass into plots where bunchgrasses, perennial forbs or annual forbs had been removed. Bunchgrasses and forbs differed in timing, depth and chemical form of N capture, and these patterns of N partitioning were not affected by soil water content. However, when we incorporated abundance (biomass) with these relative measures of N capture to determine N sequestration by the community there was no evidence suggesting that functional groups partitioned different soil N pools. Instead, dominant bunchgrasses acquired the most N from all soil N pools. Consistent with these findings we also found that bunchgrasses were the only functional group that inhibited annual grass establishment. At natural levels of species abundance, N partitioning may facilitate coexistence but may not necessarily contribute to N sequestration and invasion resistance by the plant community. This suggests that a general mechanism of invasion resistance may not be expected across systems. Instead, the key mechanism of invasion resistance within a system may depend on trait variation among coexisting species and on how species abundance is distributed in the system.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the coronavirus disease (COVID-19), is shed in feces and the virus RNA is detectable in wastewater. A nine-week wastewater epidemiology study of ten wastewater facilities, serving 39% of the state of Utah or 1.26M individuals was conducted in April and May of 2020. COVID-19 cases were tabulated from within each sewershed boundary by public health partners. The virus was detectable in 61% of 126 unique wastewater samples. Urban sewersheds serving >100,000 individuals and tourist communities had higher detection frequencies of the virus RNA. An outbreak of COVID-19 across two communities correlated with an increase in SARS-CoV-2 RNA in wastewater, while a decline in COVID-19 case counts preceded a decline in SARS-CoV-2 RNA. These results demonstrate the utility of wastewater epidemiology to assist in public health responses to COVID-19.

No abstract

Halophytes are plants that are adapted to grow in saline soils, and have been widely studied for their physiological and molecular characteristics, but little is known about their associated microbiomes. Bacteria were isolated from the rhizosphere and as root endophytes of Salicornia rubra, Sarcocornia utahensis, and Allenrolfea occidentalis , three native Utah halophytes. A total of 41 independent isolates were identified by 16S rRNA gene sequencing analysis. Isolates were tested for maximum salt tolerance, and some were able to grow in the presence of up to 4 M NaCl. Pigmentation, Gram stain characteristics, optimal temperature for growth, and biofilm formation of each isolate aided in species identification. Some variation in the bacterial population was observed in samples collected at different times of the year, while most of the genera were present regardless of the sampling time. Halomonas , Bacillus , and Kushneria species were consistently isolated both from the soil and as endophytes from roots of all three plant species at all collection times. Non-culturable bacterial species were analyzed by Illumina DNA sequencing. The most commonly identified bacteria were from several phyla commonly found in soil or extreme environments: Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, and Gamma- and Delta-Proteobacteria. Isolates were tested for the ability to stimulate growth of alfalfa under saline conditions. This screening led to the identification of one Halomonas and one Bacillus isolate that, when used to inoculate young alfalfa seedlings, stimulate plant growth in the presence of 1% NaCl, a level that significantly inhibits growth of uninoculated plants. The same bacteria used in the inoculation were recovered from surface sterilized alfalfa roots, indicating the ability of the inoculum to become established as an endophyte. The results with these isolates have exciting promise for enhancing the growth of inoculated alfalfa in salty soil.

Roots influence root litter decomposition through multiple belowground processes. Hydraulic lift or redistribution (HR) by plants is one such process that creates diel drying-rewetting cycles in soil. However, it is unclear if this phenomenon influences decomposition. Since decomposition in deserts is constrained by low soil moisture and is stimulated when dry soils are rewetted, we hypothesized that diel drying-rewetting, via HR, stimulates decomposition of root litter. We quantified the decomposition of root litter from two desert shrubs, Artemisia tridentata ssp. tridentata and Sarcobatus vermiculatus, during spring and summer in field soil core treatments designed to have abundant roots and high magnitude HR cycles (DenseRoot) or few roots and low magnitude HR (SparseRoot). To help explain our decomposition results, we not only evaluated HR, but multiple factors (i.e., soil moisture, soil temperature, dissolved soil organic C concentrations, and litter chemistry) that are often influenced by roots and regulate decomposition. Root length density in the DenseRoot treatment was at least four times higher than in the SparseRoot treatment for both Artemisia and Sarcobatus by the beginning of spring. During spring and summer, there was only one instance when decomposition rates differed between the treatments. This occurred in soils beneath Artemisia in the summer when decomposition rates were 25% higher in the DenseRoot than in the SparseRoot treatments. Of the factors evaluated, only a threefold increase in the magnitude of drying-rewetting cycles created by HR in the DenseRoot compared to the SparseRoot treatment coincided with this change in decomposition. Additionally, the lower soil W w present in the Artemisia DenseRoot treatment should have resulted in a decline in decomposition rates, but the presence of higher magnitude HR cycles seemed to nullify this effect. There was no evidence of this result in Sarcobatus soils, possibly due to Sarcobatus only creating HR cycles for a short period of time in the summer before soil W w dropped below -7 MPa. As hypothesized, our results suggest that the presence of high magnitude HR cycles stimulated decomposition. The most plausible mechanism for this stimulation; however, was not solely due to HR drying-rewetting cycles but HR creating a diel rhythm of root-driven water fluxes and rhizodeposition. These together heightened microbial activity and, subsequently, enhanced the decomposition of surrounding litter. Our findings are the first field data supporting suggestions that HR influences belowground ecosystem processes and demonstrates that this relationship is seasonally variable.