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

From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology

Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning

Attenuated variants of Lesch-Nyhan disease

Lesch–Nyhan disease is a neurogenetic disorder caused by deficiency of the enzyme hypoxanthine–guanine phosphoribosyltransferase. The classic form of the disease is described by a characteristic syndrome that includes overproduction of uric acid, severe generalized dystonia, cognitive disability and self-injurious behaviour. In addition to the classic disease, variant forms of the disease occur wherein some clinical features are absent or unusually mild. The current studies provide the results of a prospective and multi-centre international study focusing on neurological manifestations of the largest cohort of Lesch–Nyhan disease variants evaluated to date, with 46 patients from 3 to 65 years of age coming from 34 families. All had evidence for overproduction of uric acid. Motor abnormalities were evident in 42 (91%), ranging from subtle clumsiness to severely disabling generalized dystonia. Cognitive function was affected in 31 (67%) but it was never severe. Though none exhibited self-injurious behaviours, many exhibited behaviours that were maladaptive. Only three patients had no evidence of neurological dysfunction. Our results were compared with a comprehensive review of 78 prior reports describing a total of 127 Lesch–Nyhan disease variants. Together these results define the spectrum of clinical features associated with hypoxanthine–guanine phosphoribosyltransferase deficiency. At one end of the spectrum are patients with classic Lesch–Nyhan disease and the full clinical phenotype. At the other end of the spectrum are patients with overproduction of uric acid but no apparent neurological or behavioural deficits. Inbetween are patients with varying degrees of motor, cognitive, or behavioural abnormalities. Recognition of this spectrum is valuable for understanding the pathogenesis and diagnosis of all forms of hypoxanthine–guanine phosphoribosyltransferase deficiency

Acute and constitutive increases in central serotonin levels reduce social play behaviour in peri-adolescent rats

Item does not contain fulltextRATIONALE: Serotonin is an important modulator of social behaviour. Individual differences in serotonergic signalling are considered to be a marker of personality that is stable throughout lifetime. While a large body of evidence indicates that central serotonin levels are inversely related to aggression and sexual behaviour in adult rats, the relationship between serotonin and social behaviour during peri-adolescence has hardly been explored. OBJECTIVE: To study the effect of acute and constitutive increases in serotonin neurotransmission on social behaviour in peri-adolescent rats. MATERIALS AND METHODS: Social behaviour in peri-adolesent rats (28-35 days old) was studied after genetic ablation of the serotonin transporter, causing constitutively increased extra-neuronal serotonin levels, and after acute treatment with the serotonin reuptake inhibitor fluoxetine or the serotonin releasing agent 3,4-methylenedioxymethamphetamine (MDMA). A distinction was made between social play behaviour that mainly occurs during peri-adolescence, and non-playful social interactions that are abundant during the entire lifespan of rats. RESULTS: In serotonin transporter knockout rats, social play behaviour was markedly reduced, while non-playful aspects of social interaction were unaffected. Acute treatment with fluoxetine or MDMA dose-dependently inhibited social play behaviour. MDMA also suppressed non-playful social interaction but at higher doses than those required to reduce social play. Fluoxetine did not affect non-playful social interaction. CONCLUSIONS: These data show that both acute and constitutive increases in serotonergic neurotransmission reduce social play behaviour in peri-adolescent rats. Together with our previous findings of reduced aggressive and sexual behaviour in adult serotonin transporter knockout rats, these data support the notion that serotonin modulates social behaviour in a trait-like manner

Harnessing the NEON data revolution to advance open environmental science with a diverse and data-capable community

It is a critical time to reflect on the National Ecological Observatory Network (NEON) science to date as well as envision what research can be done right now with NEON (and other) data and what training is needed to enable a diverse user community. NEON became fully operational in May 2019 and has pivoted from planning and construction to operation and maintenance. In this overview, the history of and foundational thinking around NEON are discussed. A framework of open science is described with a discussion of how NEON can be situated as part of a larger data constellation—across existing networks and different suites of ecological measurements and sensors. Next, a synthesis of early NEON science, based on >100 existing publications, funded proposal efforts, and emergent science at the very first NEON Science Summit (hosted by Earth Lab at the University of Colorado Boulder in October 2019) is provided. Key questions that the ecology community will address with NEON data in the next 10 yr are outlined, from understanding drivers of biodiversity across spatial and temporal scales to defining complex feedback mechanisms in human–environmental systems. Last, the essential elements needed to engage and support a diverse and inclusive NEON user community are highlighted: training resources and tools that are openly available, funding for broad community engagement initiatives, and a mechanism to share and advertise those opportunities. NEON users require both the skills to work with NEON data and the ecological or environmental science domain knowledge to understand and interpret them. This paper synthesizes early directions in the community’s use of NEON data, and opportunities for the next 10 yr of NEON operations in emergent science themes, open science best practices, education and training, and community building

Microbiology in the Critical Zone: Examining Subsoil Microbial Responses to Wildfire and Snowmelt in Mediating Terrestrial Biogeochemical Cycles and Integrating Across Spatial and Temporal Scales

Understanding the temporal and depth-related spatial controls on microbial functional redundancy and community interactions remains a central issue in microbial ecology and Critical Zone science. Microorganisms are influenced by and influence biogeochemical reactions in the soil profile, interacting with soil, water, air, and rock throughout the Critical Zone. Snowmelt driven pulses of water and nutrients structure microbial communities, influencing rates of microbial nutrient cycling and fluctuations of greenhouse gases in forest soils. Wildfires shape the biogeochemistry of a landscape, and burn history is prevalent in US Southwestern mixed-conifer forests. Fire disturbance impacts soil and microbial communities both directly and indirectly. Fire can impact soil functioning and structure through removal of organic matter, alteration of soil structure and porosity, loss of carbon, erosion, and marked alteration of microbial community through surface burning. Indirect effects include alterations to the soil physicochemical environment and vegetation cover, impacting regional watershed functions directly immediately after fire and indirectly through changes in landscape and nutrient loadings. Subsoils hold a substantial amount of carbon that exists in both organic and inorganic forms and are sensitive to changes in temperature, moisture and disturbance regimes. Subsoils are understudied reservoirs of microbial activity and understanding the integrated interactions of microorganisms throughout the soil profile with the soil physical, chemical environment is a key component of this research. The contributions of moisture, substrate, topographic, depth and temperature controls on microbial nutrient cycling throughout the soil profile in a high elevation forest were assessed in a zero-order basin (ZOB, approximately 16 ha) located in the Jemez River Basin Critical Zone Observatory (JRB-CZO) in northern New Mexico that experienced a mixed-severity burn in 2013. Integrated and co-located measurements of bulk soil, soil gas, soil porewater and stream water chemistry measurements were taken from 2013-2017 to assess the influence of burn status, ecosystem recovery, and seasonal snowmelt dynamics and subsoil biogeochemical processes. To determine the immediate post-fire disturbance impacts on microbial functionality 22 soil pits were excavated to 40 cm and measured potential activities of seven hydrolytic enzymes involved in carbon (C), nitrogen (N), phosphorus (P) acquisition. Fire resulted in decreased activity for select carbon and nitrogen degrading enzymes in surface (0-2 cm) soils and altered N and P acquisition strategies with depth suggesting potential nutrient scavenging or increased internal microbial cycling with depth as a response to fire. Digital soil mapping demonstrated consistently higher potential enzyme activities in the convergent zones of the catchment, which were primarily correlated with higher soil moisture, clay content, and vegetative cover as quantified through normalized difference vegetation index (NDVI). Controls over enzyme activity differed in surface vs. subsurface soils where physical interactions with clay and moisture became more important in deeper soils. Seasonal pulses in water and solutes create selective pressures on resident microbiota, affecting nutrient cycling and CZ processes. The goal of the second study was to understand the relative contributions of moisture, substrate, topographic, depth, and temperature controls on microbial nutrient cycling throughout the soil profile in a high elevation forested watershed with respect to seasonality. To this end, samples were collected from two depths (0-10 cm and 30-40 cm) at 4 time points - during snowmelt, before-, during- and after the monsoon season - over multiple years across an instrumented watershed. The dissolved organic C and N pools, microbial biomass, microbial exoenzyme activities involved in C, N, and P cycling were measured to understand microbial contribution to water-driven pulses influence changes in microbial ecological traits through time and the resulting influence of watershed biogeochemical signals. Concentrations of dissolved nitrogen peaked during the spring snowmelt event. CO2 respiration peaked during the growing season but was evident under snowpack and at deeper depths. Dissolved organic carbon, nitrogen and bulk DNA concentrations increased during the summer growing season. Increase in specific enzyme activities of carbon- and nitrogen-acquiring enzymes peaked during the fall senescence period and spring snowmelt event. It was hypothesized that there would be a seasonal trade-off between growth and resource acquisition. Indeed, a key finding from this study was a positive correlation between microbial biomass carbon and dissolved organic carbon and a negative correlation between specific enzyme activity and dissolved organic carbon that varied as a function of seasonality and depth, providing further evidence for the yield-acquisition-stress trait trade-off framework. As increase in plant available labile carbon compounds increased in the growing season, so too did microbial biomass and, conversely, up regulation of enzymes involved in C and N acquisition increased as available carbon decreased. This study demonstrates how seasonality and snowmelt influence trade off of microbial ecological traits through time that impact distribution and response of mobile solute fluxes (e.g. nitrogen). These responses are important for understanding community level functional ecological dynamics in high-elevation forested catchments.The mechanisms that underly soil respiration vs. weathering were determined by analyzing soil gas CO2 and O2 ratios from soil for four years post fire recovery and with respect to seasonality. Snowmelt is an important contributor to water storage and nutrient cycling, and drives subsurface weathering dynamics. Measurements of soil CO2 and O2 were used to determine biogeochemical processes in soil in order to calculate the apparent respiratory quotient (ARQ). Deviations from ARQ=1 indicate when other processes besides aerobic respiration and diffusion control gas concentrations. When ARQ 1, processes that result in CO2 release govern. A key finding from this study revealed evidence for increased respiration in subsurface soils immediately following wildfire disturbance. This was consistent with the elevated enzyme activities observed in the previous study and potential for nutrient scavenging in subsurface soils as organic matter is volatilized in surface soil and mineral soil layer becomes exposed. As the ecosystem began to recover, and plants began to establish, the fluorescence indices of organic matter (FI) and humification degree (HIX) increased, propagating downward driving the subsurface snowmelt driven chemical weathering front. Overall, the interactions of surface vs subsurface CZ processes and their responses is not well understood, and key insights were revealed through this research showing the dynamic interactions between microbes and the soil physical and chemical environment in an ecosystem undergoing post-fire recover. This research demonstrates how fire impacts nutrient cycling in the subsurface, how seasonality and snowmelt influence tradeoffs in microbial ecological traits through time, and how processes that govern soil carbon storage, release and transport are altered as a function of fire disturbance, seasonality, and vegetation recovery. Collectively, these results lead to a greater understanding of the dynamic and interacting feedbacks between surface and subsurface soil properties that influence the distribution and responses of carbon throughout the soil profile, impacting critical zone structure and function. As a variety of global change stressors continue to escalate, understanding how the subsoil responds will become increasingly important in understanding ecosystem carbon balance