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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.

Long-term environmental research networks are one approach to advancing local, regional, and global environmental science and education. A remarkable number and wide variety of environmental research networks operate around the world today. These are diverse in funding, infrastructure, motivating questions, scientific strengths, and the sciences that birthed and maintain the networks. Some networks have individual sites that were selected because they had produced invaluable long-term data, while other networks have new sites selected to span ecological gradients. However, all long-term environmental networks share two challenges. Networks must keep pace with scientific advances and interact with both the scientific community and society at large. If networks fall short of successfully addressing these challenges, they risk becoming irrelevant. The objective of this paper is to assert that the biogeosciences offer environmental research networks a number of opportunities to expand scientific impact and public engagement. We explore some of these opportunities with four networks: the International Long-Term Ecological Research Network programs (ILTERs), critical zone observatories (CZOs), Earth and ecological observatory networks (EONs), and the FLUXNET program of eddy flux sites. While these networks were founded and expanded by interdisciplinary scientists, the preponderance of expertise and funding has gravitated activities of ILTERs and EONs toward ecology and biology, CZOs toward the Earth sciences and geology, and FLUXNET toward ecophysiology and micrometeorology. Our point is not to homogenize networks, nor to diminish disciplinary science. Rather, we argue that by more fully incorporating the integration of biology and geology in long-term environmental research networks, scientists can better leverage network assets, keep pace with the ever-changing science of the environment, and engage with larger scientific and public audiences.

The critical zone (CZ), the dynamic living skin of the Earth, extends from the top of the vegetative canopy through the soil and down to fresh bedrock and the bottom of the groundwater. All humans live in and depend on the CZ. This zone has three co-evolving surfaces: the top of the vegetative canopy, the ground surface, and a deep subsurface below which Earth's materials are unweathered. The network of nine CZ observatories supported by the US National Science Foundation has made advances in three broad areas of CZ research relating to the co-evolving surfaces. First, monitoring has revealed how natural and anthropogenic inputs at the vegetation canopy and ground surface cause subsurface responses in water, regolith structure, minerals, and biotic activity to considerable depths. This response, in turn, impacts aboveground biota and climate. Second, drilling and geophysical imaging now reveal how the deep subsurface of the CZ varies across landscapes, which in turn influences aboveground ecosystems. Third, several new mechanistic models now provide quantitative predictions of the spatial structure of the subsurface of the CZ.Many countries fund critical zone observatories (CZOs) to measure the fluxes of solutes, water, energy, gases, and sediments in the CZ and some relate these observations to the histories of those fluxes recorded in landforms, biota, soils, sediments, and rocks. Each US observatory has succeeded in (i) synthesizing research across disciplines into convergent approaches; (ii) providing long-term measurements to compare across sites; (iii) testing and developing models; (iv) collecting and measuring baseline data for comparison to catastrophic events; (v) stimulating new process-based hypotheses; (vi) catalyzing development of new techniques and instrumentation; (vii) informing the public about the CZ; (viii) mentoring students and teaching about emerging multidisciplinary CZ science; and (ix) discovering new insights about the CZ. Many of these activities can only be accomplished with observatories. Here we review the CZO enterprise in the United States and identify how such observatories could operate in the future as a network designed to generate critical scientific insights. Specifically, we recognize the need for the network to study network-level questions, expand the environments under investigation, accommodate both hypothesis testing and monitoring, and involve more stakeholders. We propose a driving question for future CZ science and a hubs-and-campaigns model to address that question and target the CZ as one unit. Only with such integrative efforts will we learn to steward the life-sustaining critical zone now and into the future.

Land use changes and reforestation impact soil phosphorus (P) distribution over extended periods. This study examines P distribution in forest development from 1957 to 2017 at the Calhoun Critical Zone Observatory in South Carolina. Tracking changes in 0–60 cm mineral soil P fractions through six samplings in eight continuously uncut plots and eight plots cut in 2007 (replanted in 2009), we hypothesized an increase in soil organic P (Po) over time in uncut plots, at the expense of HCl‐extractable P (i.e., Ca‐P). This hypothesis is based on the expectation of a transfer of P from easily accessible forms, possibly from historic fertilization to organic reservoirs within the soil. Meanwhile, we expect to lose Po in cut plots due to disturbance and residue decomposition, and increase bioavailable Mehlich‐III extractable P (Mehlich‐III P), resin inorganic phosphorus (Pi), and HCO3 Pi. Results revealed a continued decrease in Mehlich‐III P in uncut (38.7–15.7 µg g−1) and cut plots (25.2–17.7 µg g−1) within the 0–7.5 cm range. NaOH‐Po in uncut plots remained stable, while in cut plots, it increased by ∼4 µg g−1 in the 0–7.5 cm soil layer. Slowly cycling Po (NaOH‐Po) increased during forest regrowth in the cut plots, aligning with rising soil organic carbon and decreasing soil pH. Soil P changes indicate minor declines in available fractions during the initial three decades, with the HCl extractable (Ca‐P) fraction experiencing the highest depletion. In the later three decades, P associated with NaOH extraction (i.e., iron [Fe] and aluminum [Al] bound P) declined, although estimated mineral soil P removals during this period were less than accumulated P in tree biomass and forest floor. The total soil P decline from 1990 to 2017 was 34 kg ha−1, suggesting a growing role of P recycling from debris decomposition in supplying soil P to plants. Core Ideas: Phosphorus distribution in mineral soils is dynamic across a forest's developmental timeline from 1957 to 2017.Phosphorus recycling from forest floor and soil organic P contributes to plant nutrient supply.An agricultural fertilization legacy is still influencing long‐term phosphorus cycling.The decadal timescale of this study highlights the role of slowly cycling phosphorus fractions over extended time scales. [ABSTRACT FROM AUTHOR]

Present understanding of the global carbon cycle is limited by uncertainty over soil-carbon dynamics. The clearing of the world's forests, mainly for agricultural uses, releases large amounts of carbon to the atmosphere (up to 2 x 1015 gyr-1), much of which arises from the cultivation driving an accelerated decomposition of soil organic matter. Although the effects of cultivation on soil carbon are well studied, studies of soil-carbon recovery after cultivation are limited. Here we present a four-decade-long field study of carbon accumulation by pine ecosystems established on previously cultivated soils in South Carolina, USA. Newly accumulated carbon is tracked by its distinctive 14C signature, acquired around the onset of forest growth from thermonuclear bomb testing that nearly doubled atmospheric 14CO2 in the 1960s. Field data combined with model simulations indicate that the young aggrading forest rapidly incorporated bomb radiocarbon into the forest floor and the upper 60 cm of underlying mineral soil. By the 1990s, however, carbon accumulated only in forest biomass, forest floor, and the upper 7.5 cm of the mineral soil. Although the forest was a strong carbon sink, trees accounted for about 80%, the forest floor 20%, and mineral soil

This study investigates mechanisms that generate regularly spaced iron-rich bands in upland soils. These striking features appear in soils worldwide, but beyond a generalized association with changing redox, their genesis is yet to be explained. Upland soils exhibit significant redox fluctuations driven by rainfall, groundwater changes, or irrigation. Pattern formation in such systems provides an opportunity to investigate the temporal aspects of spatial self-organization, which have been heretofore understudied. By comparing multiple alternative mechanisms, we found that regular iron banding in upland soils is explained by coupling two sets of scale-dependent feedbacks, the general principle of Turing morphogenesis. First, clay dispersion and coagulation in iron redox fluctuations amplify soil Fe(III) aggregation and crystal growth to a level that negatively affects root growth. Second, the activation of this negative root response to highly crystalline Fe(III) leads to the formation of rhythmic iron bands. In forming iron bands, environmental variability plays a critical role. It creates alternating anoxic and oxic conditions for required pattern-forming processes to occur in distinctly separated times and determines durations of anoxic and oxic episodes, thereby controlling relative rates of processes accompanying oxidation and reduction reactions. As Turing morphogenesis requires ratios of certain process rates to be within a specific range, environmental variability thus modifies the likelihood that pattern formation will occur. Projected changes of climatic regime could significantly alter many spatially self-organized systems, as well as the ecological functioning associated with the striking patterns they present. This temporal dimension of pattern formation merits close attention in the future. [ABSTRACT FROM AUTHOR]