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The global carbon cycle is experiencing continued perturbations via increases in atmospheric carbon concentrations, which are partly reduced by terrestrial biosphere and ocean carbon uptake. Greenhouse gas satellites have been shown to be useful in retrieving atmospheric carbon concentrations and observing surface and atmospheric CO2 seasonal-to-interannual variations. However, limited attention has been placed on using satellite column CO2 retrievals to evaluate surface CO2 fluxes from the terrestrial biosphere without advanced inversion models at low latency. Such applications could be useful to monitor, in near real time, biosphere carbon fluxes during climatic anomalies like drought, heatwaves, and floods, before more complex terrestrial biosphere model outputs and/or advanced inversion modelling estimates become available. Here, we explore the ability of Orbiting Carbon Observatory-2 (OCO-2) column-averaged dry air CO2 (XCO2) retrievals to directly detect and estimate terrestrial biosphere CO2 flux anomalies using a simple mass-balance approach. An initial global analysis of surface–atmospheric CO2 coupling and transport conditions reveals that the western US, among a handful of other regions, is a feasible candidate for using XCO2 for detecting terrestrial biosphere CO2 flux anomalies. Using the CarbonTracker model reanalysis as a test bed, we first demonstrate that a well-established mass-balance approach can estimate monthly surface CO2 flux anomalies from XCO2 enhancements in the western United States. The method is optimal when the study domain is spatially extensive enough to account for atmospheric mixing and has favorable advection conditions with contributions primarily from one background region. We find that errors in individual soundings reduce the ability of OCO-2 XCO2 to estimate more frequent, smaller surface CO2 flux anomalies. However, we find that OCO-2 XCO2 can often detect and estimate large surface flux anomalies that leave an imprint on the atmospheric CO2 concentration anomalies beyond the retrieval error/uncertainty associated with the observations. OCO-2 can thus be useful for low-latency monitoring of the monthly timing and magnitude of extreme regional terrestrial biosphere carbon anomalies.

With a changing climate, it is becoming increasingly critical to understand vegetation responses to limiting environmental factors. Here, we investigate the spatial and temporal patterns of light and water limitation on photosynthesis using an observational framework. Our study is unique in characterizing the nonlinear relationships between photosynthesis and water and light, acknowledging approximately two regime behaviours (no limitation and varying degrees of limitation). It is also unique in using an observational framework instead of using model-derived photosynthesis properties. We combine data from three different satellite sensors, i.e., sun-induced chlorophyll fluorescence (SIF) from the TROPOspheric Monitoring Instrument (TROPOMI), surface soil moisture from the Soil Moisture Active Passive (SMAP) microwave radiometer, and vegetation greenness from the Moderate Resolution Imaging Spectroradiometer (MODIS). We find both single-regime and two-regime models describe SIF sensitivity to soil moisture and photosynthetically active radiation (PAR) across the globe. The distribution and strength of soil moisture limitation on SIF are mapped in the water-limited environments, while the distribution and strength of PAR limitations are mapped in the energy-limited environments. A two-regime behaviour is detected in 73 % of the cases for water limitation on photosynthesis, while two-regime detection is much lower at 41 % for light limitation on photosynthesis. SIF sensitivity to PAR strongly increases along moisture gradients, reflecting mesic vegetation's adaptation to making rapid usage of incoming light availability on the weekly timescales. The transition point detected between the two regimes is connected to soil type and mean annual precipitation for the SIF–soil moisture relationship and for the SIF–PAR relationship. These thresholds therefore have an explicit relation to properties of the landscape, although they may also be related to finer details of the vegetation and soil interactions not resolved by the spatial scales here. The simple functions and thresholds are emergent behaviours capturing the interaction of many processes. The observational thresholds and strength of coupling can be used as benchmark information for Earth system models, especially those that characterize gross primary production mechanisms and vegetation dynamics.

Plant hydraulic and photosynthetic responses to individual rain pulses are not well understood because field experiments of pulse behavior are sparse. Understanding individual pulse responses would inform how rainfall intermittency impacts terrestrial biogeochemical cycles, especially in drylands, which play a large role in interannual global atmospheric carbon uptake variability. Using satellite-based estimates of predawn plant and soil water content from the Soil Moisture Active Passive (SMAP) satellite, we quantify the timescales of plant water content increases following rainfall pulses, which we expect bear the signature of whole-plant mechanisms. In wetter regions, we find that plant water content increases rapidly and dries along with soil moisture, which we attribute to predawn soil–plant water potential equilibrium. Global drylands, by contrast, show multi-day plant water content increases after rain pulses. Shorter increases are more common following dry initial soil conditions. These are attributed to slow plant rehydration due to high plant resistances using a plant hydraulic model. Longer multi-day dryland plant water content increases are attributed to pulse-driven growth, following larger rain pulses and wetter initial soil conditions. These dryland responses reflect widespread drought recovery rehydration responses and individual pulse-driven growth responses, as supported by previous isolated field experiments. The response dependence on moisture pulse characteristics, especially in drylands, also shows ecosystem sensitivity to intra-annual rainfall intensity and frequency, which are shifting with climate change.

Abstract During extensive periods without rain, known as dry-downs, decreasing soil moisture (SM) induces plant water stress at the point when it limits evapotranspiration, defining a critical SM threshold (θcrit). Better quantification of θcrit is needed for improving future projections of climate and water resources, food production, and ecosystem vulnerability. Here, we combine systematic satellite observations of the diurnal amplitude of land surface temperature (dLST) and SM during dry-downs, corroborated by in-situ data from flux towers, to generate the observation-based global map of θcrit. We find an average global θcrit of 0.19 m3/m3, varying from 0.12 m3/m3 in arid ecosystems to 0.26 m3/m3 in humid ecosystems. θcrit simulated by Earth System Models is overestimated in dry areas and underestimated in wet areas. The global observed pattern of θcrit reflects plant adaptation to soil available water and atmospheric demand. Using explainable machine learning, we show that aridity index, leaf area and soil texture are the most influential drivers. Moreover, we show that the annual fraction of days with water stress, when SM stays below θcrit, has increased in the past four decades. Our results have important implications for understanding the inception of water stress in models and identifying SM tipping points.

Abstract Dryland ecosystems cover 40% of our planet's land surface, support billions of people, and are responding rapidly to climate and land use change. These expansive systems also dominate core aspects of Earth's climate, storing and exchanging vast amounts of water, carbon, and energy with the atmosphere. Despite their indispensable ecosystem services and high vulnerability to change, drylands are one of the least understood ecosystem types, partly due to challenges studying their heterogeneous landscapes and misconceptions that drylands are unproductive “wastelands.” Consequently, inadequate understanding of dryland processes has resulted in poor model representation and forecasting capacity, hindering decision making for these at‐risk ecosystems. NASA satellite resources are increasingly available at the higher resolutions needed to enhance understanding of drylands' heterogeneous spatiotemporal dynamics. NASA's Terrestrial Ecology Program solicited proposals for scoping a multi‐year field campaign, of which Adaptation and Response in Drylands (ARID) was one of two scoping studies selected. A primary goal of the scoping study is to gather input from the scientific and data end‐user communities on dryland research gaps and data user needs. Here, we provide an overview of the ARID team's community engagement and how it has guided development of our framework. This includes an ARID kickoff meeting with over 300 participants held in October 2023 at the University of Arizona to gather input from data end‐users and scientists. We also summarize insights gained from hundreds of follow‐up activities, including from a tribal‐engagement focused workshop in New Mexico, conference town halls, intensive roundtables, and international engagements.

Abstract Vegetation optical depth (VOD) satellite microwave retrievals provide significant insights into vegetation water content and responses to hydroclimatic changes. While VOD variations are commonly linked to dry biomass and live fuel moisture content (LFMC), the impact of canopy temperature (Tc) remains overlooked in large‐scale studies. Here, we investigated the impact of Tc on L‐band (1.4 GHz) and X‐band (10.7 GHz) VOD at diurnal and seasonal timescales. Synthetic benchmark VOD was created using realistic fields of Tc, LFMC, and biomass in an electromagnetic model. Perturbation experiments revealed that Tc strongly affects diurnal VOD variations at both L‐band and X‐band. Seasonally, while biomass emerges as the largest contributor to VOD variations in 70% (at X‐band) and 90% (at L‐band) of our study region, Tc and LFMC still play substantial roles. The findings stress the importance of refining retrieval algorithms to distinguish Tc, LFMC, and biomass effects for future VOD applications in ecohydrology.

Abstract Satellite‐retrieved vegetation optical depth (VOD) has provided extensive insights into global plant function (such as, carbon stocks, water stress, crop yields) because of VOD's ability to monitor plant water stress and biomass at near daily temporal frequency under all‐weather conditions. However, arguably, the greatest challenge with broadly applying VOD is its lack of validation partly because of VOD's simultaneous sensitivity to plant water status and biomass changes, as well as intensive methods required to measure these properties in‐situ. Here, inspired by the recent Yao et al. (2024), https://doi.org/10.1029/2023GL107121 article, I argue that VOD estimated from global navigation satellite systems (GNSS) and land surface models with plant hydraulic schemes are two emerging methods that show promise for more widely validating satellite‐based VOD. I encourage wider adoption of these approaches to validate and further advance satellite‐based VOD research.

Abstract While remote sensing has provided extensive insights into the global terrestrial water, carbon, and energy cycles, space‐based retrievals remain limited in observing the belowground influence of the full soil moisture (SM) profile on ecosystem function. We show that this gap can be addressed when coupling 70 m resolution ECOsystem Spaceborne Thermal Radiometer Experiment on Space Station retrievals of land surface temperature (LST) with in‐situ SM profile measurements. These data sets together reveal that ecosystem water use decreases with depth with 93% of sites showing significant LST coupling with SM shallower than 20 cm while 34% of sites have interactions with SM deeper than 50 cm. Furthermore, the median depth of peak ecosystem water use is estimated to be 10 cm, though forests have more common peak interactions with deeper soil layers (50–100 cm) in 37% of cases. High spatial resolution remote sensing coupled with field‐level data can thus elucidate the role of belowground processes on land surface behavior.

Satellite-based soil moisture products allow direct monitoring of agricultural drought, especially in regions with sparse ground-based observations. In this study, a soil moisture drought index only based on satellite soil moisture is developed and adopted to assess drought in Mainland Southeast Asia (MSA). We report here on an exceptionally severe Mainland Southeast Asia drought in 2016, which is believed to be strongly linked to the 2015–2016 super El Niño strongly. The event began in February 2016 and lasted until May 2016, with more than 50% of the study areas suffering from moderate drought or worse at peak period. We assess the evolution of agricultural droughts (defined as prolonged deficit in soil moisture) by placing it in the context of the forcing meteorological drought (prolonged deficit in precipitation). The drought assessment using satellite soil moisture is temporally consistent with precipitation-based metrics, but allows for better mapping of the spatial and temporal patterns of how a precipitation deficit may or may not lead to a soil moisture deficit. The specific advantages of a remote-sensing approach—wide-coverage without need for spatially-dense, ground-based climatological records, and sensitivity to otherwise unmeasured irrigation inputs—suggest further opportunity for drought monitoring in ungauged regions, particularly in agricultural contexts.

Nosocomial pathogens of the Acinetobacter calcoaceticus-baumannii (ACB) complex are a cautionary example for the world-wide spread of multi- and pan-drug resistant bacteria. Aiding the urgent demand for novel therapeutic targets, comparative genomics studies between pathogens and their apathogenic relatives shed light on the genetic basis of human-pathogen interaction. Yet, existing studies are limited in taxonomic scope, sensing of the phylogenetic signal, and resolution by largely analyzing genes independent of their organization in functional gene clusters. Here, we explored more than 3,000 Acinetobacter genomes in a phylogenomic framework integrating orthology-based phylogenetic profiling and microsynteny conservation analyses. We delineate gene clusters in the type strain A. baumannii ATCC 19606 whose evolutionary conservation indicates a functional integration of the subsumed genes. These evolutionarily stable gene clusters (ESGCs) reveal metabolic pathways, transcriptional regulators residing next to their targets but also tie together sub-clusters with distinct functions to form higher-order functional modules. We shortlisted 150 ESGCs that either co-emerged with the pathogenic ACB clade or are preferentially found therein. They provide a high-resolution picture of genetic and functional changes that coincide with the manifestation of the pathogenic phenotype in the ACB clade. Key innovations are the remodeling of the regulatory-effector cascade connecting LuxR/LuxI quorum sensing via an intermediate messenger to biofilm formation, the extension of micronutrient scavenging systems, and the increase of metabolic flexibility by exploiting carbon sources that are provided by the human host. We could show experimentally that only members of the ACB clade use kynurenine as a sole carbon and energy source, a substance produced by humans to fine-tune the antimicrobial innate immune response. In summary, this study provides a rich and unbiased set of novel testable hypotheses on how pathogenic Acinetobacter interact with and ultimately infect their human host. It is a comprehensive resource for future research into novel therapeutic strategies.

ABSTRACT Approximately one-third of the human colonic microbiome is formed by bacteria from the genus Bacteroides. These bacteria produce a large amount of uniformly sized outer membrane vesicles (OMVs), which are equipped with hydrolytic enzymes that play a role in the degradation of diet- and host-derived glycans. In this work, we characterize the lipid composition of membranes and OMVs from Bacteroides thetaiotaomicron VPI-5482. Liquid chromatography-mass spectrometry (LC-MS) analysis indicated that OMVs carry sphingolipids, glycerophospholipids, and serine-dipeptide lipids. Sphingolipid species represent more than 50% of the total lipid content of OMVs. The most abundant sphingolipids in OMVs are ethanolamine phosphoceramide (EPC) and inositol phosphoceramide (IPC). Bioinformatics analysis allowed the identification of the BT1522–1526 operon putatively involved in IPC synthesis. Mutagenesis studies revealed that BT1522–1526 is essential for the synthesis of phosphatidylinositol (PI) and IPC, confirming the role of this operon in the biosynthesis of IPC. BT1522–1526 mutant strains lacking IPC produced OMVs that were indistinguishable from the wild-type strain, indicating that IPC sphingolipid species are not involved in OMV biogenesis. Given the known role of sphingolipids in immunomodulation, we suggest that OMVs may act as long-distance vehicles for the delivery of sphingolipids in the human gut. IMPORTANCE Sphingolipids are essential membrane lipid components found in eukaryotes that are also involved in cell signaling processes. Although rare in bacteria, sphingolipids are produced by members of the phylum Bacteroidetes, human gut commensals. Here, we determined that OMVs carry sphingolipids and other lipids of known signaling function. Our results demonstrate that the BT1522–1526 operon is required for IPC biosynthesis in B. thetaiotaomicron.

Multidrug-resistant Acinetobacter baumannii infections are increasing at alarming rates. Therefore, novel antibiotic-sparing treatments to combat these A. baumannii infections are urgently needed. The development of these interventions would benefit from a better understanding of this bacterium's pathobiology, which remains poorly understood. A. baumannii is regarded as an extracellular opportunistic pathogen. However, research on Acinetobacter has largely focused on common lab strains, such as ATCC 19606, that have been isolated several decades ago. These strains exhibit reduced virulence when compared to recently isolated clinical strains. In this work, we demonstrate that, unlike ATCC 19606, several modern A. baumannii clinical isolates, including the recent clinical urinary isolate UPAB1, persist and replicate inside macrophages within spacious vacuoles. We show that intracellular replication of UPAB1 is dependent on a functional type I secretion system (T1SS) and pAB5, a large conjugative plasmid that controls the expression of several chromosomally-encoded genes. Finally, we show that UPAB1 escapes from the infected macrophages by a lytic process. To our knowledge, this is the first report of intracellular growth and replication of A. baumannii. We suggest that intracellular replication within macrophages may contribute to evasion of the immune response, dissemination, and antibiotic tolerance of A. baumannii.

Acinetobacter baumannii is generally considered an opportunistic pathogen. Here, Di Venanzio et al. develop a mouse model of catheter-associated urinary tract infection and show that a plasmid confers niche specificity to an A. baumannii urinary isolate by regulating the expression of chromosomal genes.

Bioconjugation is a promising process to manufacture conjugate vaccines, but currently employed enzymes cannot generate the full spectrum of bacterial glycoproteins. Here, the authors use an O-linking oligosaccharyltransferase to generate a polyvalent pneumococcal bioconjugate vaccine with polysaccharides containing glucose at their reducing end.

ABSTRACT Glycans decorate proteins and affect their biological function, including protection against proteolytic degradation. However, pathogenic, and commensal bacteria have evolved specific glycoproteases that overcome the steric impediment posed by carbohydrates, cleaving glycoproteins precisely at their glycosylation site(s). Medically relevant Acinetobacter strains employ their type II secretion system (T2SS) to secrete the glycoprotease CpaA, which contributes to virulence. Previously, CpaA was shown to cleave two O-linked glycoproteins, factors V and XII, leading to reduced blood coagulation. In this work, we show that CpaA cleaves a broader range of O-linked human glycoproteins, including several glycoproteins involved in complement activation, such as CD55 and CD46. However, only CD55 was removed from the cell surface, while CD46 remained unaltered during the Acinetobacter nosocomialis infection assay. We show that CpaA has a unique consensus target sequence that consists of a glycosylated serine or threonine residue after a proline residue (P-S/T), and its activity is not affected by sialic acids. Molecular modeling and mutagenesis analysis of CpaA suggest that the indole ring of Trp493 and the ring of the Pro residue in the substrate form a key interaction that contributes to CpaA sequence selectivity. Similar bacterial glycoproteases have recently gained attention as tools for proteomic analysis of human glycoproteins, and CpaA appears to be a robust and attractive new component of the glycoproteomics toolbox. Combined, our work provides insight into the function and possible application of CpaA, a member of a widespread class of broad-spectrum bacterial glycoproteases involved in host-pathogen interactions. IMPORTANCE CpaA is a glycoprotease expressed by members of the Acinetobacter baumannii-calcoaceticus complex, and it is the first bona fide secreted virulence factor identified in these species. Here, we show that CpaA cleaves multiple targets precisely at O-glycosylation sites preceded by a Pro residue. This feature, together with the observation that sialic acid does not impact CpaA activity, makes this enzyme an attractive tool for the analysis of O-linked human protein for biotechnical and diagnostic purposes. Previous work identified proteins involved in blood coagulation as targets of CpaA. Our work broadens the set of targets of CpaA, pointing toward additional roles in bacterium-host interactions. We propose that CpaA belongs to an expanding class of functionally defined glycoproteases that targets multiple O-linked host glycoproteins.

ABSTRACT The type VI secretion system (T6SS) is a critical weapon in bacterial warfare between Gram-negative bacteria. Although invaluable for niche establishment, this machine represents an energetic burden to its host bacterium. Acinetobacter baumannii is an opportunistic pathogen that poses a serious threat to public health due to its high rates of multidrug resistance. In some A. baumannii strains, the T6SS is transcriptionally downregulated by large multidrug resistance plasmids. Other strains, such as the clinical isolate AbCAN2, express T6SS-related genes but lack T6SS activity under laboratory conditions, despite not harboring these plasmids. This suggests that alternative mechanisms exist to repress the T6SS. Here, we used a transposon mutagenesis approach in AbCAN2 to identify novel T6SS repressors. Our screen revealed that the T6SS of this strain is inhibited by a homolog of VgrG, an essential structural component of all T6SSs reported to date. We named this protein inhibitory VgrG (VgrGi). Biochemical and in silico analyses demonstrated that the unprecedented inhibitory capability of VgrGi is due to a single amino acid mutation in a widely conserved C-terminal domain of unknown function, DUF2345. We also show that unlike in other bacteria, the C terminus of VgrG is essential for functional T6SS assembly in A. baumannii. Our study provides insight into the architectural requirements underlying functional assembly of the T6SS of A. baumannii. We propose that T6SS-inactivating point mutations are beneficial to the host bacterium, since they eliminate the energy cost associated with maintaining a functional T6SS, which appears to be unnecessary for A. baumannii virulence. IMPORTANCE Despite the clinical relevance of A. baumannii, little is known about its fundamental biology. Here, we show that a single amino acid mutation in VgrG, a critical T6SS structural protein, abrogates T6SS function. Given that this mutation was found in a clinical isolate, we propose that the T6SS of A. baumannii is probably not involved in virulence; this idea is supported by multiple genomic analyses showing that the majority of clinical A. baumannii strains lack proteins essential to the T6SS. We also show that, unlike in other species, the C terminus of VgrG is a unique architectural requirement for functional T6SS assembly in A. baumannii, suggesting that over evolutionary time, bacteria have developed changes to their T6SS architecture, leading to specialized systems.

Protein secretion plays a crucial role for bacterial pathogens, exemplified by facultative human-pathogen Vibrio cholerae, which secretes various proteinaceous effectors at different stages of its lifecycle. Accordingly, the identification of factors impacting on protein secretion is important to understand the bacterial pathophysiology. PglLVc, a predicted oligosaccharyltransferase of V. cholerae, has been recently shown to exhibit O-glycosylation activity with relaxed glycan specificity in an engineered Escherichia coli system. By engineering V. cholerae strains to express a defined, undecaprenyl diphosphate-linked glycoform precursor, we confirmed functional O-linked protein glycosylation activity of PglLVc in V. cholerae. We demonstrate that PglLVc is required for the glycosylation of multiple V. cholerae proteins, including periplasmic chaperones such as DegP, that are required for efficient type II-dependent secretion. Moreover, defined deletion mutants and complementation strains provided first insights into the physiological role of O-linked protein glycosylation in V. cholerae. RbmD, a protein with structural similarities to PglLVc and other established oligosaccharyltransferases (OTases), was also included in this phenotypical characterization. Remarkably, presence or absence of PglLVc and RbmD impacts the secretion of proteins via the type II secretion system (T2SS). This is highlighted by altered cholera toxin (CT) secretion, chitin utilization and biofilm formation observed in ΔpglLVc and ΔrbmD single or double mutants. This work thus establishes a unique connection between broad spectrum O-linked protein glycosylation and the efficacy of type II-dependent protein secretion critical to the pathogen’s lifecycle.

ABSTRACT Outer membrane vesicles (OMVs) are spherical structures derived from the outer membranes (OMs) of Gram-negative bacteria. Bacteroides spp. are prominent components of the human gut microbiota, and OMVs produced by these species are proposed to play key roles in gut homeostasis. OMV biogenesis in Bacteroides is a poorly understood process. Here, we revisited the protein composition of Bacteroides thetaiotaomicron OMVs by mass spectrometry. We confirmed that OMVs produced by this organism contain large quantities of glycosidases and proteases, with most of them being lipoproteins. We found that most of these OMV-enriched lipoproteins are encoded by polysaccharide utilization loci (PULs), such as the sus operon. We examined the subcellular locations of the components of the Sus system and found a split localization; the alpha-amylase SusG is highly enriched in OMVs, while the oligosaccharide importer SusC remains mostly in the OM. We found that all OMV-enriched lipoproteins possess a lipoprotein export sequence (LES), and we show that this signal mediates translocation of SusG from the periplasmic face of the OM toward the extracellular milieu. Mutations in the LES motif caused defects in surface exposure and recruitment of SusG into OMVs. These experiments link, for the first time, surface exposure to recruitment of proteins into OMVs. We also show that surface-exposed SusG in OMVs is active and rescues the growth of bacterial cells incapable of growing on starch as the only carbon source. Our results support the role of OMVs as “public goods” that can be utilized by other organisms with different metabolic capabilities. IMPORTANCE Species from the Bacteroides genus are predominant members of the human gut microbiota. OMVs in Bacteroides have been shown to be important for the homeostasis of complex host-commensal relationships, mainly involving immune tolerance and protection from disease. OMVs carry many enzymatic activities involved in the cleavage of complex polysaccharides and have been proposed as public goods that can provide growth to other bacterial species by release of polysaccharide breakdown products into the gut lumen. This work shows that the presence of a negatively charged rich amino acid motif (LES) is required for efficient packing of the surface-exposed alpha-amylase SusG into OMVs. Our findings strongly suggest that surface exposure is coupled to packing of Bacteroides lipoproteins into OMVs. This is the first step in the generation of tailor-made probiotic interventions that can exploit LES-related sequences to generate Bacteroides strains displaying proteins of interest in OMVs.

Bacteria release outer membrane vesicles (OMVs) that play important roles in pathogenesis and intercellular interactions. Here, Roier et al. provide evidence supporting that phospholipid accumulation in the outer leaflet of the outer membrane participates in OMV formation in Gram-negative bacteria.