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Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.

Deserts comprise a large portion of the Earth's land area, yet their role in the fluxes and cycles of greenhouse gases is poorly known and their likely response to climate change largely unexplored. We report a reconnaissance investigation of the concentrations and fluxes of CO2, CH4, and N2O along two elevation (climate) gradients in the southwestern United States. In-soil concentrations of CO2 increased with elevation (up to 5,000 ppm). Concentrations of CH4 declined with depth in all soils (to less than 1 ppm), but the rates of decrease with depth increased with elevation. In contrast, concentrations and depth trends of N2O varied erratically. Soils were net CO2 sources (0 to >1,500 kg CO2·ha−1·year−1), and net CH4 sinks (0.2 to >3 kg CH4·ha−1·year−1). The small and variable N2O fluxes were inconsistent with the trends in soil N δ15N values, which decreased by 5‰ to 6‰ over about 1,000 m of elevation. The high soil N δ15N values (up to nearly 17‰ at the lowest elevation) indicate that there is a soil N loss mechanism that is highly depleted in 15N, and gaseous losses—either NH3 or N2O/N2—are suspected of driving these values. In summary, there appears to be a strong climate control on both soil CO2 and CH4 concentrations and to a lesser degree on calculated fluxes. The soil N trace gas concentrations indicate that deserts can be either small sources or sinks of N2O and that there may be significant consumption of arid soil N2O.

Although once thought to be devoid of biology, recent studies have identified salt deposits as oases for life in the hyperarid Atacama Desert. To examine spatial patterns of microbial species and key nutrient sources, we genomically characterized 26 salt crusts from three sites along a fog gradient. The communities are dominated by a large variety of Halobacteriales and Bacteroidetes, plus a few algal and Cyanobacterial species. CRISPR locus analysis suggests the distribution of a single Cyanobacterial population among all sites. This is in stark contrast to the extremely high sample specificity of most other community members. Only present at the highest moisture site is a genomically characterized Thermoplasmatales archaeon (Marine Group II) and six Nanohaloarchaea, one of which is represented by a complete genome. Parcubacteria (OD1) and Saccharibacteria (TM7), not previously reported from hypersaline environments, were found at low abundances. We found no indication of a N2 fixation pathway in the communities, suggesting acquisition of bioavailable nitrogen from atmospherically derived nitrate. Samples cluster by site based on bacterial and archaeal abundance patterns and photosynthetic capacity decreases with increasing distance from the ocean. We conclude that moisture level, controlled by coastal fog intensity, is the strongest driver of community membership.

The tree of life is one of the most important organizing principles in biology(1). Gene surveys suggest the existence of an enormous number of branches(2), but even an approximation of the full scale of the tree has remained elusive. Recent depictions of the tree of life have focused either on the nature of deep evolutionary relationships(3-5) or on the known, well-classified diversity of life with an emphasis on eukaryotes(6). These approaches overlook the dramatic change in our understanding of life's diversity resulting from genomic sampling of previously unexamined environments. New methods to generate genome sequences illuminate the identity of organisms and their metabolic capacities, placing them in community and ecosystem contexts(7,8). Here, we use new genomic data from over 1,000 uncultivated and little known organisms, together with published sequences, to infer a dramatically expanded version of the tree of life, with Bacteria, Archaea and Eukarya included. The depiction is both a global overview and a snapshot of the diversity within each major lineage. The results reveal the dominance of bacterial diversification and underline the importance of organisms lacking isolated representatives, with substantial evolution concentrated in a major radiation of such organisms. This tree highlights major lineages currently underrepresented in biogeochemical models and identifies radiations that are probably important for future evolutionary analyses.

Our understanding of climatic conditions, and therefore forcing factors, in North America during the past two glacial cycles is limited in part by the scarcity of long, well-dated, continuous paleoclimate records. Here, we present the first, to our knowledge, continuous, millennial-resolution paleoclimate proxy record derived from millimeter-thick pedogenic carbonate clast coatings (pedothems), which are widely distributed in semiarid to arid regions worldwide. Our new multiisotope pedothem record from the Wind River Basin in Wyoming confirms a previously hypothesized period of increased transport of Gulf of Mexico moisture northward into the continental interior from 70,000 to 55,000 years ago based on oxygen and carbon isotopes determined by ion microprobe and uranium isotopes and U-Th dating by laser ablation inductively coupled plasma mass spectrometry. This pronounced meridional moisture transport, which contrasts with the dominant zonal transport of Pacific moisture into the North American interior by westerly winds before and after 70,000-55,000 years ago, may have resulted from a persistent anticyclone developed above the North American ice sheet during Marine Isotope Stage 4. We conclude that pedothems, when analyzed using microanalytical techniques, can provide high-resolution paleoclimate records that may open new avenues into understanding past terrestrial climates in regions where paleoclimate records are not otherwise available. When pedothem paleoclimate records are combined with existing records they will add complimentary soil-based perspectives on paleoclimate conditions.

Human security has and will continue to rely on Earth's diverse soil resources. Yet we have now exploited the planet's most productive soils. Soil erosion greatly exceeds rates of production in many agricultural regions. Nitrogen produced by fossil fuel and geological reservoirs of other fertilizers are headed toward possible scarcity, increased cost, and/or geopolitical conflict. Climate change is accelerating the microbial release of greenhouse gases from soil organic matter and will likely play a large role in our near-term climate future. In this Review, we highlight challenges facing Earth's soil resources in the coming century. The direct and indirect response of soils to past and future human activities will play a major role in human prosperity and survival.

Human security has and will continue to rely on Earth's diverse soil resources. Yet we have now exploited the planet's most productive soils. Soil erosion greatly exceeds rates of production in many agricultural regions. Nitrogen produced by fossil fuel and geological reservoirs of other fertilizers are headed toward possible scarcity, increased cost, and/or geopolitical conflict. Climate change is accelerating the microbial release of greenhouse gases from soil organic matter and will likely play a large role in our near-term climate future. In this Review, we highlight challenges facing Earth's soil resources in the coming century. The direct and indirect response of soils to past and future human activities will play a major role in human prosperity and survival.

Measurements of CO2 flux, soil temperature, and moisture content of selected natural and disturbed soils in central California were made on a monthly basis from August 1994 to October 1995 in an attempt to detect the effects of temperature, moisture, and land use change on CO2 production in soils. Soil CO2 flux displayed a strong negative correlation with soil temperature and a positive correlation with soil moisture at the natural site. However, at the disturbed site, the linear correlation between CO2 flux and temperature/moisture was insignificant. The negative correlation between soil CO2 flux and soil temperature is in contrast to what has been observed in other ecosystems but is typical for Mediterranean ecosystems in which grasses are biologically active only during cool months. Comparison of carbon (C) inventories of paired natural and disturbed soils indicates that both cultivation and logging have resulted in a significant decrease in total soil C content. The reduction in soil C storage is about 26% for the cultivated soil and around 30% for the logged soil. Most of the C loss is from the upper horizons. Radiocarbon (14C) measurements of both recent and archived soil samples demonstrate large differences in C input rate and turnover time between natural and disturbed soils. The average turnover times of organic matter are longer in disturbed soils than in the corresponding natural soils as a result of preferential loss of C from “active” soil C pools. In both natural and disturbed soils, the average turnover times of organic matter increase with depth from decades or less in shallow horizons to hundreds of years or even thousands of years in deeper horizons. Our results show that land use change can have significant impact on soil C cycle and that shallow soil horizons are most susceptible to disturbance because of shorter turnover times of organic C in these horizons.

The article "Climate change mitigation through soil carbon sequestration in working lands: A reality check" questions the validity and realism of claims made by Almaraz et al. regarding the potential magnitude of soil carbon sequestration (SCS) in agricultural soils. The authors argue that Almaraz et al. overestimate the availability of organic matter for compost and biochar, inaccurately interpret carbon sequestration rates, and make premature assumptions about the applicability of enhanced rock weathering. They emphasize the need for realistic evaluations of the limitations and trade-offs of SCS practices and caution against overly optimistic estimates that can mislead policymakers. The authors declare no conflicts of interest. [Extracted from the article]

Radiocarbon ages of soil organic matter are evaluated with a model which incorporates the dynamics of the 14C content of soil organic matter. Measured 14C ages of soil organic matter or its fractions are always younger than the true ages of soils due to continuous input of organic matter into soils. Differences in soil C dynamics due to climate or soil depth will result in significantly different 14C signatures of soil organic matter for soils of the same age. As a result, the deviation of the measured 14C age from the true age of soil formation could differ significantly among different soils or soil horizons. Our model calculations also suggest that 14C ages of soil organic matter will eventually reach a steady state provided that no climatic or ecological perturbations occur. Once a soil or a soil horizon has reached a steady state, 14C dating of soil organic matter will provide no useful information regarding the age of the soil. However, for soils in which steady state has not been reached, it is possible to estimate the age of soil formation by modeling the measured 14C contents of soil organic matter. Radiocarbon dating of buried soils could, in general, overestimate the true age of the burial by as much as the steady-state age of the soil or soil horizon. © 1996 University of Washington.

The stable N and O isotope composition of soil and soil‐respired N2O is increasingly measured, yet a solid theoretical framework for interpreting the data remains to be developed. Here, the physical processes that affect soil N2O and its isotopes are embedded in a diffusion/reaction model. Numerical experiments are compared to data to demonstrate how various soil processes influence depth profiles and surface fluxes of soil N2O, δ15NN2O, and δ18ON2O. Model predictions and data suggest that the isotope composition of the net N2O soil flux, in soils that have N2O consumption, is a function of the net flux rate, and the isotope differences between the atmosphere and the biological source. Asymptotically large negative or positive δ15Nflux and δ18Oflux values occur as the net soil N2O flux approaches zero from positive or negative flux rates, respectively. This implies that the isotopic imprint of soil fluxes on the global atmospheric N2O pool is more variable than previously suggested. Additionally, the observed isotope values in static flux chambers are possibly complicated by the fact that consumption fluxes increase as the concentration in the chambers increases. This work reveals that even simple chamber flux measurements may possess isotope effects imparted by consumption during the chamber measurement and suggests ways to experimentally test this possibility. Additionally, simple methods to estimate depth‐dependent net production/consumption and its isotope effects are suggested. However, understanding the gross rates of the production and consumption of soil N2O remains an elusive goal. Plain Language Summary: Soils are one of the largest global emitters of the greenhouse gas nitrous oxide (N2O). Yet, unlike greenhouse gases such as carbon dioxide, the emission patterns bear weak linkages to climatic patterns. One reason for this may be that the N2O that finally escapes soil is the residue of much larger rates of microbial production that are counterbalanced by large rates of consumption. Here, we use hundreds of previously published data on the concentration and stable nitrogen and oxygen isotope ratio of N2O and re‐interpret them through a physics‐based model. We find unexpected evidence that the isotope composition of the emitted N2O, which is sometimes used as a signal to estimate the total global soil emission rate, is a complex function of the balance between production and consumption, and the net flux rates. A better understanding of the conditions that may increase these consumption rates will be of value to potentially reduce soil emissions and their impact on the climate system. Key Points: Currently, there is no unified theoretical framework to interpret soil N2O isotope ratiosModel and limited empirical measurements indicate that the N and O isotope values of N2O fluxes from soils may be dependent on flux rates, and may be much more variable than previously assumedSimple calculations of observed soil N2O profiles (concentration and isotope values) can provide insights into spatial variability in the net result of N2O production and consumptive processes [ABSTRACT FROM AUTHOR]

A model is presented describing the factors and processes which determine the measured 14C ages of soil calcium carbonate. Pedogenic carbonate forms in isotopic equilium with soil CO2. Carbon dioxide in soils is a mixture of CO2 derived from two biological sources: respiration by living plant roots and respiration of microorganisms decomposing soil humus. The relative proportion of these two CO2 sources can greatly affect the initial 14C content of pedogenic carbonate: the greater the contribution of humus-derived CO2, the greater the initial 14C age of the carbonate mineral. For any given mixture of CO2 sources, the steady-state 14CO2 distribution vs. soil depth can be described by a production/diffusion model. As a soil ages, the 14C age of soil humus increases, as does the steady-state 14C age of soil CO2 and the initial 14C age of any pedogenic carbonate which forms. The mean 14C age of a complete pedogenic carbonate coating or nodule will underestimate the true age of the soil carbonate. This discrepancy increases the older a soil becomes. Partial removal of outer (and younger) carbonate coatings greatly improves the relationship between measured 14C age and true age. Although the production/diffusion model qualitatively explains the 14C age of pedogenic carbonate vs. soil depth in many soils, other factors, such as climate change, may contribute to the observed trends, particularily in soils older than the Holocene. © 1994.

A diffusion-reaction model for soil 14CO2 is described that analyzes the 14CO2 distribution in soils. It shows that the 14C content of soil CO2 is not the same as that of atmospheric CO2 and varies with depth depending on various factors. The most important factors affecting the 14C content of soil CO2 include the 14C content of soil organic matter, the relative contribution of root respired CO2 to total CO2 production, soil respiration rate, atmospheric CO2 concentration and 14CO2 content, and soil properties such as temperature and moisture content etc. The 14C content of soil CO2 not only can be a sensitive indicator of the residence time of decomposing organic matter in the soil, but also determines the 14C content of pedogenic carbonate. Our model suggests that soil CO2 could be enriched or depleted in 14C relative to atmospheric CO2, depending on the relative contribution of root respiration to total soil respiration and on the turnover rate of the soil organic matter contributing to the soil CO2. Therefore, the initial 14C dates of soil carbonate could differ from the true ages of pedogenesis. The processes and factors considered by the model are a first step in determining whether the 14C content of soil carbonate could lead to reliable dates of pedogenesis. © 1994.