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BACKGROUND AND AIMS: Crohns disease is a debilitating chronic inflammatory disorder of the mammalian gastrointestinal tract. Current interventions using anti-tumour necrosis factor [anti-TNF] biologics show long-term benefit in only half of patients. This study focused on the role of the TNF receptor 1 [TNFR1] in pathogenesis in a TNF-driven model of ileitis. METHODS: We studied TNFΔAU-rich element [ARE]/+ [TNFdARE] mice, which develop progressive ileitis similar to Crohns ileitis. Histopathological analysis and gene expression profiling were used to characterize disease progression from 5 to 16 weeks. Mice with TNFR1 hemizygosity [TNFdARE/R1het] allowed us to assess gene dosage effects. Transcriptional profiling established inflection points in disease progression; inflammatory gene expression increased at 8 weeks with a plateau by 10 weeks, so these were selected as endpoints of treatment using the TNF biologic infliximab and the TNFR1-specific XPro1595. Differences in recruitment of cells in the lamina propria were assessed using flow cytometry. RESULTS: TNFdARE/R1het mice displayed stable long-term protection from disease, associated with decreased recruitment of CD11bhiF4/80lo monocytes and CD11bhiLy6Ghi neutrophils, suggesting an important role of TNFR1 signalling in pathogenesis, and indicating potential benefit from TNFR1-specific intervention. Treatment with infliximab and XPro1595 both showed a similar impact on disease in TNFdARE mice. Importantly, these beneficial effects were greatly surpassed by hemizygosity at the TNFR1 locus. CONCLUSIONS: Treatment with either infliximab or XPro1595 produced moderate protection from ileitis in TNFdARE mice. However, hemizygosity at the TNFR1 locus in TNFdARE mice showed far better protection, implicating TNFR1 signalling as a key mediator of TNF-driven disease.

Although the Salton Sea was once a thriving destination for humans and wildlife, it has now degraded to the point of ecosystem collapse. Increases in local dust emissions have introduced aeolian (wind-blown) microorganisms that travel, along with contaminants and minerals, into the atmosphere, detrimentally impacting inhabitants of the region. Proliferation of certain microbial groups in regions of the Sea may have a disproportionate impact on local ecological systems. Yet, little is known about how the biogeochemical processes of this drying lakebed influence microbial community composition and dispersal. To elucidate how these microorganisms contribute, and adapt, to the Sea's volatile conditions, we synthesize research on three niche-specific microbiomes — exposed lakebed (playa), the Sea, and aeolian — and highlight modern molecular techniques, such as metagenomics, coupled with physical science methodologies, including transport modeling, to predict how the drying lakebed will affect microbial processes. We argue that an explicit consideration of microbial groups within this system is needed to provide vital information about the distribution and functional roles of ecologically pertinent microbial groups. Such knowledge could help inform regulatory measures aimed at restoring the health of the Sea's human and ecological systems.

The Salton Sea is a drying salt lake in an arid region with high aerosol particulate-matter concentrations. This region is plagued by a high incidence of asthma, attributed in part to the aerosols surrounding the Sea. But the connection between the Sea and asthma may be more than simple calculations of dust concentrations. While dusts might contain toxic substances that impact the lungs of residents, the complex dynamics related to the environmental degradation of the Salton Sea may be generating additional toxins relevant to public health, such as microcystins produced by algal blooms. This collection of pollutants may be driving inflammatory responses in the lungs of residents through multiple mechanisms. As such, examination of the full range of potential environmental triggers of lung inflammation promises to yield a better understanding of key mechanisms driving the high incidence of asthma in local residents. Our discussion provides a perspective aiming to re-frame the issue in the context of the historical theory of “miasma” and the linkages between environmental change and health impacts.

Dust provides an ecologically significant input of nutrients, especially in slowly eroding ecosystems where chemical weathering intensity limits nutrient inputs from underlying bedrock. In addition to nutrient inputs, incoming dust is a vector for dispersing dust-associated microorganisms. While little is known about dust-microbial dispersal, dust deposits may have transformative effects on ecosystems far from where the dust was emitted. Using molecular analyses, we examined spatiotemporal variation in incoming dust microbiomes along an elevational gradient within the Sierra Nevada of California. We sampled throughout two dry seasons and found that dust microbiomes differed by elevation across two summer dry seasons (2014 and 2015), which corresponded to competing droughts in dust source areas. Dust microbial taxa richness decreased with elevation and was inversely proportional to dust heterogeneity. Likewise, dust phosphorus content increased with elevation. At lower elevations, early season dust microbiomes were more diverse than those found later in the year. The relative abundances of microbial groups shifted during the summer dry season. Furthermore, mutualistic fungal diversity increased with elevation, which may have corresponded with the biogeography of their plant hosts. Although dust fungal pathogen diversity was equivalent across elevations, elevation and sampling month interactions for the relative abundance, diversity, and richness of fungal pathogens suggest that these pathogens differed temporally across elevations, with potential implications for humans and wildlife. This study shows that landscape topography and droughts in source locations may alter the composition and diversity of ecologically relevant dust-associated microorganisms.

Ambigolimax valentianus is an invasive European terrestrial gastropod distributed throughout California. It is a serious pest of gardens, plant nurseries, and greenhouses. We evaluated the bacterial microbiome of whole slugs to capture a more detailed picture of bacterial diversity and composition in this host. We concentrated on the influences of diet and environment on the Ambigolimax valentianus core bacterial microbiome as a starting point for obtaining valuable information to aid in future slug microbiome studies. Ambigolimax valentianus were collected from two environments (gardens or reared from eggs in a laboratory). DNA from whole slugs were extracted and next-generation 16S rRNA gene sequencing was performed. Slug microbiomes differed between environmental sources (garden- vs. lab-reared) and were influenced by a sterile diet. Lab-reared slugs fed an unsterile diet harbored greater bacterial species than garden-reared slugs. A small core microbiome was present that was shared across all slug treatments. This is consistent with our hypothesis that a core microbiome is present and will not change due to these treatments. Findings from this study will help elucidate the impacts of slug-assisted bacterial dispersal on soils and plants, while providing valuable information about the slug microbiome for potential integrated pest research applications.

Feedbacks between plants and surrounding soil microbes can contribute to the establishment and persistence of invasive annual grasses as well as limit the success of restoration efforts. In this study, we aim to understand how three sources of soil inocula – native, invasive (from under Bromus diandrus) and sterile – affect the growth response and fungal community composition in the roots of a chaparral shrub, Adenostoma fasciculatum. We grew A. fasciculatum from seed in a greenhouse with each inoculum source and harvested at six months. We measured above- and below-ground biomass, arbuscular mycorrhizal fungal (AMF) colonization and conducted targeted-amplicon sequencing of the 18S and ITS2 loci to characterize AMF and general fungal community composition, respectively. Native inoculum resulted in roots with richer communities of some groups of AMF and non-AMF symbionts, when compared to roots grown with invasive or sterile inoculum. Seedlings grown with invasive and native inoculum did not have different growth responses, but both produced more biomass than a sterile control. These findings suggest that inoculation with soil from native species can increase the diversity of multiple groups of fungal symbionts and inoculation with live soil (invasive or native) can increase seedling biomass. Moreover, future work would benefit from assessing if a more diverse community of fungal symbionts increases seedling survival when planted in field restoration sites.

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.

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.

Habitat fragmentation is widespread across ecosystems, detrimentally affecting biodiversity. Although most habitat fragmentation studies have been conducted on macroscopic organisms, microbial communities and fungal processes may also be threatened by fragmentation. This study investigated whether fragmentation, and the effects of fragmentation on plants, altered fungal diversity and function within a fragmented shrubland in southern California. Using fluorimetric techniques, we assayed enzymes from plant litter collected from fragments of varying sizes to investigate enzymatic responses to fragmentation. To isolate the effects of plant richness from those of fragment size on fungi, we deployed litter bags containing different levels of plant litter diversity into the largest fragment and incubated in the field for one year. Following field incubation, we determined litter mass loss and conducted molecular analyses of fungal communities. We found that leaf-litter enzyme activity declined in smaller habitat fragments with less diverse vegetation. Moreover, we detected greater litter mass loss in litter bags containing more diverse plant litter. Additionally, bags with greater plant litter diversity harbored greater numbers of fungal taxa. These findings suggest that both plant litter resources and fungal function may be affected by habitat fragmentation's constraints on plants, possibly because plant species differ chemically, and may thus decompose at different rates. Diverse plant assemblages may produce a greater variety of litter resources and provide more ecological niche space, which may support greater numbers of fungal taxa. Thus, reduced plant diversity may constrain both fungal taxa richness and decomposition in fragmented coastal shrublands. Altogether, our findings provide evidence that even fungi may be affected by human-driven habitat fragmentation via direct effects of fragmentation on plants. Our findings underscore the importance of restoring diverse vegetation communities within larger coastal sage scrub fragments and suggest that this may be an effective way to improve the functional capacity of degraded sites.

Few studies have investigated how soil fungal communities respond to elevation, especially within TMCF (tropical montane cloud forests). We used an elevation gradient in a TMCF in Costa Rica to determine how soil properties, processes, and community composition of fungi change in response to elevation and across seasons. As elevation increased, soil temperature and soil pH decreased, while soil moisture and soil C:N ratios increased with elevation. Responses of these properties varied seasonally. Fungal abundance increased with elevation during wet and dry seasons. Fungal community composition shifted in response to elevation, and to a lesser extent by season. These shifts were accompanied by varying responses of important fungal functional groups during the wet season and the relative abundance of certain fungal phyla. We suggest that elevation and the responses of certain fungal functional groups may be structuring fungal communities along this elevation gradient. TMCF are ecosystems that are rapidly changing due to climate change. Our study suggests that these changes may affect how fungal communities are structured.

Although fungal communities are known to vary along latitudinal gradients, mechanisms underlying this pattern are not well-understood. We used high-throughput sequencing to examine the large-scale distributions of soil fungi and their relation to evolutionary history. We tested the Tropical Conservatism Hypothesis, which predicts that ancestral fungal groups should be more restricted to tropical latitudes and conditions than would more recently derived groups. We found support for this hypothesis in that older phyla preferred significantly lower latitudes and warmer, wetter conditions than did younger phyla. Moreover, preferences for higher latitudes and lower precipitation levels were significantly phylogenetically conserved among the six younger phyla, possibly because the older phyla possess a zoospore stage that is vulnerable to drought, whereas the younger phyla retain protective cell walls throughout their life cycle. Our study provides novel evidence that the Tropical Conservatism Hypothesis applies to microbes as well as plants and animals.

Abstract: We tested the hypothesis that field applications of arbuscular mycorrhizal (AM) inocula would increase root colonization and plant performance in a coastal sage scrub (CSS) restoration project in Southern [...]

Purpose: Substantial studies report about the extent of elevated CO2 (eCO2) and nitrogenous (N) fertilization or deposition above- and belowground. Although CO2 concentrations are expected to be more than 1000 μmol·mol−1 by 2100 (IPCC 2014), there are relatively few studies about the effects of highly concentrated eCO2 plus N fertilization on woody plants. Materials and methods: Schima superba seedlings were exposed to eCO2 and N fertilization in open-top chambers (OTCs), including ambient air (400 μmol·mol−1), 550, 750, and 1000 μmol mol−1 and 5, 10, or 0 g N m−2·year−1, respectively. Plant photosynthesis (Pn), leaf/root carbon (C) and N, and biomass were analyzed; furthermore, soil microbial community structure was examined. Results and discussion: After only one growing season, the combination of eCO2 and N fertilization increased Pn. N fertilization also increased plant biomass. The combined effect of higher CO2 concentration with N fertilization further stimulated plant biomass. Soil fungal community structure was altered by eCO2 via affecting leaf N and C/N. Moreover, N fertilization changed the composition of soil bacterial communities, which in part was driven by soil NO3−, as well as root C/N. Although eCO2 and N fertilization yielded a direct relationship of synergistic effects on Pn and plant biomass, they elicited contrasting effects on soil copiotrophic and oligotrophic groups, which mediate the soil microbial community structure and nutrient cycling. Conclusions: Plant growth and soil microbial communities could be affected within short time scales by global change. Experimental manipulations that focus on the singular effects of either CO2 or N fertilization alone may underestimate the effects of global change on woody plants. [ABSTRACT FROM AUTHOR]

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