Integrating airborne remote sensing and field campaigns for ecology and Earth system science
Not Available
54 ENVIRONMENTAL SCIENCES↗
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Results for “ecological trait”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi
Abstract Background Linking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists. Of many techniques that strive for this goal, Stable-isotope probing—SIP—remains among the most comprehensive for studying whole microbial communities in situ. In DNA-SIP, actively growing microorganisms that take up an isotopically heavy substrate build heavier DNA, which can be partitioned by density into multiple fractions and sequenced. However, SIP is relatively low throughput and requires significant hands-on labor. We designed and tested a semi-automated, high-throughput SIP (HT-SIP) pipeline to support well-replicated, temporally resolved amplicon and metagenomics experiments. We applied this pipeline to a soil microhabitat with significant ecological importance—the hyphosphere zone surrounding arbuscular mycorrhizal fungal (AMF) hyphae. AMF form symbiotic relationships with most plant species and play key roles in terrestrial nutrient and carbon cycling. Results Our HT-SIP pipeline for fractionation, cleanup, and nucleic acid quantification of density gradients requires one-sixth of the hands-on labor compared to manual SIP and allows 16 samples to be processed simultaneously. Automated density fractionation increased the reproducibility of SIP gradients compared to manual fractionation, and we show adding a non-ionic detergent to the gradient buffer improved SIP DNA recovery. We applied HT-SIP to 13 C-AMF hyphosphere DNA from a 13 CO 2 plant labeling study and created metagenome-assembled genomes (MAGs) using high-resolution SIP metagenomics (14 metagenomes per gradient). SIP confirmed the AMF Rhizophagus intraradices and associated MAGs were highly enriched (10–33 atom% 13 C), even though the soils’ overall enrichment was low (1.8 atom% 13 C). We assembled 212 13 C-hyphosphere MAGs; the hyphosphere taxa that assimilated the most AMF-derived 13 C were from the phyla Myxococcota, Fibrobacterota, Verrucomicrobiota, and the ammonia-oxidizing archaeon genus Nitrososphaera . Conclusions Our semi-automated HT-SIP approach decreases operator time and improves reproducibility by targeting the most labor-intensive steps of SIP—fraction collection and cleanup. We illustrate this approach in a unique and understudied soil microhabitat—generating MAGs of actively growing microbes living in the AMF hyphosphere (without plant roots). The MAGs’ phylogenetic composition and gene content suggest predation, decomposition, and ammonia oxidation may be key processes in hyphosphere nutrient cycling.
59 BASIC BIOLOGICAL SCIENCES↗
A framework for integrating genomics, microbial traits, and ecosystem biogeochemistry
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
The temperature sensitivity of soil: microbial biodiversity, growth, and carbon mineralization
Abstract Microorganisms drive soil carbon mineralization and changes in their activity with increased temperature could feedback to climate change. Variation in microbial biodiversity and the temperature sensitivities (Q10) of individual taxa may explain differences in the Q10 of soil respiration, a possibility not previously examined due to methodological limitations. Here, we show phylogenetic and taxonomic variation in the Q10 of growth (5–35 °C) among soil bacteria from four sites, one from each of Arctic, boreal, temperate, and tropical biomes. Differences in the temperature sensitivities of taxa and the taxonomic composition of communities determined community-assembled bacterial growth Q10, which was strongly predictive of soil respiration Q10 within and across biomes. Our results suggest community-assembled traits of microbial taxa may enable enhanced prediction of carbon cycling feedbacks to climate change in ecosystems across the globe.
Wang, Chao (ORCID:0000000257567505)↗
Hydraulic safety and growth rather than climate of origin influence survival in desert shrubs and trees
The species-poor woodlands and forests in arid regions are particularly vulnerable to climate change induced plant die-off. Searching for species suitable to replant in these areas is an effective way to prevent further expansion of land desertification. Good knowledge of drought resistance of species is critical for current replanting efforts, however, the related plant survival mechanisms in the process of restoration remain limited. Here, we tested the dominant drivers of plant survival in relation to climate factors, growth characteristics and functional traits including hydraulics and gas exchange across 35 multiple shrub and tree woody species in a common garden at the Tengger Desert, northwest China. We found the desert plants had a wide range of hydraulic thresholds among these desert species, with relative high hydraulic safety, and low xylem hydraulic conductivity. Pant survival was largely determined by hydraulic safety and growth status, but was not affected by the climate of the species’ site of origin. Shrubs and trees diverged in hydraulic and growth characteristics, while there was no difference between native and introduced species. In this study, our results highlight the critical roles of hydraulic safety and growth on determining the survival and drought adaptation during desert vegetation development, which provide a new insight into ecological restoration in arid regions under changing climate conditions.
54 ENVIRONMENTAL SCIENCES↗
Decadal changes in fire frequencies shift tree communities and functional traits
Global change has resulted in chronic shifts in fire regimes. Variability in the sensitivity of tree communities to multi-decadal changes in fire regimes is critical to anticipating shifts in ecosystem structure and function, yet remains poorly understood. Here, we address the overall effects of fire on tree communities and the factors controlling their sensitivity in 29 sites that experienced multi-decadal alterations in fire frequencies in savanna and forest ecosystems across tropical and temperate regions. Fire had a strong overall effect on tree communities, with an average fire frequency (one fire every three years) reducing stem density by 48% and basal area by 53% after 50 years, relative to unburned plots. Here, the largest changes occurred in savanna ecosystems and in sites with strong wet seasons or strong dry seasons, pointing to fire characteristics and species composition as important. Analyses of functional traits highlighted the impact of fire-driven changes in soil nutrients because frequent burning favoured trees with low biomass nitrogen and phosphorus content, and with more efficient nitrogen acquisition through ectomycorrhizal symbioses. Taken together, the response of trees to altered fire frequencies depends both on climatic and vegetation determinants of fire behaviour and tree growth, and the coupling between fire-driven nutrient losses and plant traits.
54 ENVIRONMENTAL SCIENCES↗
Aerobic Methoxydotrophy: Growth on Methoxylated Aromatic Compounds by Methylobacteriaceae
Pink-pigmented facultative methylotrophs have long been studied for their ability to grow on reduced single-carbon (C 1 ) compounds. The C 1 groups that support methylotrophic growth may come from a variety of sources. Here, we describe a group of Methylobacterium strains that can engage in methoxydotrophy: they can metabolize the methoxy groups from several aromatic compounds that are commonly the product of lignin depolymerization. Furthermore, these organisms can utilize the full aromatic ring as a growth substrate, a phenotype that has rarely been described in Methylobacterium . We demonstrated growth on p -hydroxybenzoate, protocatechuate, vanillate, and ferulate in laboratory culture conditions. We also used comparative genomics to explore the evolutionary history of this trait, finding that the capacity for aromatic catabolism is likely ancestral to two clades of Methylobacterium , but has also been acquired horizontally by closely related organisms. In addition, we surveyed the published metagenome data to find that the most abundant group of aromatic-degrading Methylobacterium in the environment is likely the group related to Methylobacterium nodulans , and they are especially common in soil and root environments. The demethoxylation of lignin-derived aromatic monomers in aerobic environments releases formaldehyde, a metabolite that is a potent cellular toxin but that is also a growth substrate for methylotrophs. We found that, whereas some known lignin-degrading organisms excrete formaldehyde as a byproduct during growth on vanillate, Methylobacterium do not. This observation is especially relevant to our understanding of the ecology and the bioengineering of lignin degradation.
59 BASIC BIOLOGICAL SCIENCES↗
Incubation temperature as a constraint on clutch size evolution
Not provided.
Environmental Sciences & Ecology↗
Adaptive Phenotypic Plasticity Stabilizes Evolution in Fluctuating Environments
Fluctuating environmental conditions are ubiquitous in natural systems, and populations have evolved various strategies to cope with such fluctuations. The particular mechanisms that evolve profoundly influence subsequent evolutionary dynamics. One such mechanism is phenotypic plasticity, which is the ability of a single genotype to produce alternate phenotypes in an environmentally dependent context. Here, we use digital organisms (self-replicating computer programs) to investigate how adaptive phenotypic plasticity alters evolutionary dynamics and influences evolutionary outcomes in cyclically changing environments. Specifically, we examined the evolutionary histories of both plastic populations and non-plastic populations to ask: (1) Does adaptive plasticity promote or constrain evolutionary change? (2) Are plastic populations better able to evolve and then maintain novel traits? And (3), how does adaptive plasticity affect the potential for maladaptive alleles to accumulate in evolving genomes? We find that populations with adaptive phenotypic plasticity undergo less evolutionary change than non-plastic populations, which must rely on genetic variation from de novo mutations to continuously readapt to environmental fluctuations. Indeed, the non-plastic populations undergo more frequent selective sweeps and accumulate many more genetic changes. We find that the repeated selective sweeps in non-plastic populations drive the loss of beneficial traits and accumulation of maladaptive alleles, whereas phenotypic plasticity can stabilize populations against environmental fluctuations. This stabilization allows plastic populations to more easily retain novel adaptive traits than their non-plastic counterparts. In general, the evolution of adaptive phenotypic plasticity shifted evolutionary dynamics to be more similar to that of populations evolving in a static environment than to non-plastic populations evolving in an identical fluctuating environment. All natural environments subject populations to some form of change; our findings suggest that the stabilizing effect of phenotypic plasticity plays an important role in subsequent adaptive evolution.
54 ENVIRONMENTAL SCIENCES↗
Evolutionary Analyses of Gene Expression Divergence in Panicum hallii : Exploring Constitutive and Plastic Responses Using Reciprocal Transplants
Abstract The evolution of gene expression is thought to be an important mechanism of local adaptation and ecological speciation. Gene expression divergence occurs through the evolution of cis- polymorphisms and through more widespread effects driven by trans-regulatory factors. Here, we explore expression and sequence divergence in a large sample of Panicum hallii accessions encompassing the species range using a reciprocal transplantation experiment. We observed widespread genotype and transplant site drivers of expression divergence, with a limited number of genes exhibiting genotype-by-site interactions. We used a modified FST–QST outlier approach (QPC analysis) to detect local adaptation. We identified 514 genes with constitutive expression divergence above and beyond the levels expected under neutral processes. However, no plastic expression responses met our multiple testing correction as QPC outliers. Constitutive QPC outlier genes were involved in a number of developmental processes and responses to abiotic environments. Leveraging earlier expression quantitative trait loci results, we found a strong enrichment of expression divergence, including for QPC outliers, in genes previously identified with cis and cis–environment interactions but found no patterns related to trans-factors. Population genetic analyses detected elevated sequence divergence of promoters and coding sequence of constitutive expression outliers but little evidence for positive selection on these proteins. Our results are consistent with a hypothesis of cis-regulatory divergence as a primary driver of expression divergence in P. hallii.
3′ TagSeq↗
Macroecological distributions of gene variants highlight the functional organization of soil microbial systems
Abstract The recent application of macroecological tools and concepts has made it possible to identify consistent patterns in the distribution of microbial biodiversity, which greatly improved our understanding of the microbial world at large scales. However, the distribution of microbial functions remains largely uncharted from the macroecological point of view. Here, we used macroecological models to examine how the genes encoding the functional capabilities of microorganisms are distributed within and across soil systems. Models built using functional gene array data from 818 soil microbial communities showed that the occupancy-frequency distributions of genes were bimodal in every studied site, and that their rank-abundance distributions were best described by a lognormal model. In addition, the relationships between gene occupancy and abundance were positive in all sites. This allowed us to identify genes with high abundance and ubiquitous distribution (core) and genes with low abundance and limited spatial distribution (satellites), and to show that they encode different sets of microbial traits. Common genes encode microbial traits related to the main biogeochemical cycles (C, N, P and S) while rare genes encode traits related to adaptation to environmental stresses, such as nutrient limitation, resistance to heavy metals and degradation of xenobiotics. Overall, this study characterized for the first time the distribution of microbial functional genes within soil systems, and highlight the interest of macroecological models for understanding the functional organization of microbial systems across spatial scales.
59 BASIC BIOLOGICAL SCIENCES↗
Remote Sensing of Tundra Ecosystems Using High Spectral Resolution Reflectance: Opportunities and Challenges
Abstract Observing the environment in the vast regions of Earth through remote sensing platforms provides the tools to measure ecological dynamics. The Arctic tundra biome, one of the largest inaccessible terrestrial biomes on Earth, requires remote sensing across multiple spatial and temporal scales, from towers to satellites, particularly those equipped for imaging spectroscopy (IS). We describe a rationale for using IS derived from advances in our understanding of Arctic tundra vegetation communities and their interaction with the environment. To best leverage ongoing and forthcoming IS resources, including National Aeronautics and Space Administration’s Surface Biology and Geology mission, we identify a series of opportunities and challenges based on intrinsic spectral dimensionality analysis and a review of current data and literature that illustrates the unique attributes of the Arctic tundra biome. These opportunities and challenges include thematic vegetation mapping, complicated by low‐stature plants and very fine‐scale surface composition heterogeneity; development of scalable algorithms for retrieval of canopy and leaf traits; nuanced variation in vegetation growth and composition that complicates detection of long‐term trends; and rapid phenological changes across brief growing seasons that may go undetected due to low revisit frequency or be obscured by snow cover and clouds. We recommend improvements to future field campaigns and satellite missions, advocating for research that combines multi‐scale spectroscopy, from lab studies to satellites that enable frequent and continuous long‐term monitoring, to inform statistical and biophysical approaches to model vegetation dynamics.
54 ENVIRONMENTAL SCIENCES↗
Manganese Limitation of Phytoplankton Physiology and Productivity in the Southern Ocean
Although iron and light are understood to regulate the Southern Ocean biological carbon pump, observations have also indicated a possible role for manganese. Low concentrations in Southern Ocean surface waters suggest manganese limitation is possible, but its spatial extent remains poorly constrained and direct manganese limitation of the marine carbon cycle has been neglected by ocean models. Here, using available observations, we develop a new global biogeochemical model and find that phytoplankton in over half of the Southern Ocean cannot attain maximal growth rates because of manganese deficiency. Manganese limitation is most extensive in austral spring and depends on phytoplankton traits related to the size of photosynthetic antennae and the inhibition of manganese uptake by high zinc concentrations in Antarctic waters. Importantly, manganese limitation expands under the increased iron supply of past glacial periods, reducing the response of the biological carbon pump. Overall, these model experiments describe a mosaic of controls on Southern Ocean productivity that emerge from the interplay of light, iron, manganese and zinc, shaping the evolution of Antarctic phytoplankton since the opening of the Drake Passage.
54 ENVIRONMENTAL SCIENCES↗
Development of a Miniaturized Mobile Mapping System for In-Row, Under-Canopy Phenotyping
This paper focuses on the development of a miniaturized mobile mapping platform with advantages over current agricultural phenotyping systems in terms of acquiring data that facilitate under-canopy plant trait extraction. The system is based on an unmanned ground vehicle (UGV) for in-row, under-canopy data acquisition to deliver accurately georeferenced 2D and 3D products. The paper addresses three main aspects pertaining to the UGV development: (a) architecture of the UGV mobile mapping system (MMS), (b) quality assessment of acquired data in terms of georeferencing information as well as derived 3D point cloud, and (c) ability to derive phenotypic plant traits using data acquired by the UGV MMS. The experimental results from this study demonstrate the ability of the UGV MMS to acquire dense and accurate data over agricultural fields that would facilitate highly accurate plant phenotyping (better than above-canopy platforms such as unmanned aerial systems and high-clearance tractors). Plant centers and plant count with an accuracy in the 90% range have been achieved.
54 ENVIRONMENTAL SCIENCES↗
The influence of incubation temperature on offspring traits varies across northern and southern populations of the American alligator ( Alligator mississippiensis )
Maternal provisioning and the developmental environment are fundamental determinants of offspring traits, particularly in oviparous species. However, the extent to which embryonic responses to these factors differ across populations to drive phenotypic variation is not well understood. Here, we examine the contributions of maternal provisioning and incubation temperature to hatchling morphological and metabolic traits across four populations of the American alligator (Alligator mississippiensis), encompassing a large portion of the species' latitudinal range. Our results show that whereas the influence of egg mass is generally consistent across populations, responses to incubation temperature show population-level variation in several traits, including mass, head length, head width, and residual yolk mass. Additionally, the influence of incubation temperature on developmental rate is greater at northern populations, while the allocation of maternal resources toward fat body mass is greater at southern populations. Overall, our results suggest that responses to incubation temperature, relative to maternal provisioning, are a larger source of interpopulation phenotypic variation and may contribute to the local adaptation of populations.
59 BASIC BIOLOGICAL SCIENCES↗
All the light we cannot see: Climate manipulations leave short and long‐term imprints in spectral reflectance of trees
Abstract Anthropogenic climate change, particularly changes in temperature and precipitation, affects plants in multiple ways. Because plants respond dynamically to stress and acclimate to changes in growing conditions, diagnosing quantitative plant‐environment relationships is a major challenge. One approach to this problem is to quantify leaf responses using spectral reflectance, which provides rapid, inexpensive, and nondestructive measurements that capture a wealth of information about genotype as well as phenotypic responses to the environment. However, it is unclear how warming and drought affect spectra. To address this gap, we used an open‐air field experiment that manipulates temperature and rainfall in 36 plots at two sites in the boreal‐temperate ecotone of northern Minnesota, USA. We collected leaf spectral reflectance (400–2400 nm) at the peak of the growing season for three consecutive years on juveniles (two to six years old) of five tree species planted within the experiment. We hypothesized that these mid‐season measurements of spectral reflectance capture a snapshot of the leaf phenotype encompassing a suite of physiological, structural, and biochemical responses to both long‐ and short‐time scale environmental conditions. We show that the imprint of environmental conditions experienced by plants hours to weeks before spectral measurements is linked to regions in the spectrum associated with stress, namely the water absorption regions of the near‐infrared and short‐wave infrared. In contrast, the environmental conditions plants experience during leaf development leave lasting imprints on the spectral profiles of leaves, attributable to leaf structure and chemistry (e.g., pigment content and associated ratios). Our analyses show that after accounting for baseline species spectral differences, spectral responses to the environment do not differ among the species. This suggests that building a general framework for understanding forest responses to climate change through spectral metrics may be possible, likely having broader implications if the common responses among species detected here represent a widespread phenomenon. Consequently, these results demonstrate that examining the entire spectrum of leaf reflectance for environmental imprints in contrast to single features (e.g., indices and traits) improves inferences about plant‐environment relationships, which is particularly important in times of unprecedented climate change.
Stefanski, Artur [Department of Forest Resources U↗
Life history strategies among soil bacteria—dichotomy for few, continuum for many
Abstract Study of life history strategies may help predict the performance of microorganisms in nature by organizing the complexity of microbial communities into groups of organisms with similar strategies. Here, we tested the extent that one common application of life history theory, the copiotroph-oligotroph framework, could predict the relative population growth rate of bacterial taxa in soils from four different ecosystems. We measured the change of in situ relative growth rate to added glucose and ammonium using both 18O–H2O and 13C quantitative stable isotope probing to test whether bacterial taxa sorted into copiotrophic and oligotrophic groups. We saw considerable overlap in nutrient responses across most bacteria regardless of phyla, with many taxa growing slowly and few taxa that grew quickly. To define plausible life history boundaries based on in situ relative growth rates, we applied Gaussian mixture models to organisms’ joint 18O–13C signatures and found that across experimental replicates, few taxa could consistently be assigned as copiotrophs, despite their potential for fast growth. When life history classifications were assigned based on average relative growth rate at varying taxonomic levels, finer resolutions (e.g., genus level) were significantly more effective in capturing changes in nutrient response than broad taxonomic resolution (e.g., phylum level). Our results demonstrate the difficulty in generalizing bacterial life history strategies to broad lineages, and even to single organisms across a range of soils and experimental conditions. We conclude that there is a continued need for the direct measurement of microbial communities in soil to advance ecologically realistic frameworks.
59 BASIC BIOLOGICAL SCIENCES↗
Functional traits driving species role in the structure of terrestrial vertebrate scavenger networks
Abstract Species assemblages often have a non‐random nested organization, which in vertebrate scavenger (carrion‐consuming) assemblages is thought to be driven by facilitation in competitive environments. However, not all scavenger species play the same role in maintaining assemblage structure, as some species are obligate scavengers (i.e., vultures) and others are facultative, scavenging opportunistically. We used a database with 177 vertebrate scavenger species from 53 assemblages in 22 countries across five continents to identify which functional traits of scavenger species are key to maintaining the scavenging network structure. We used network analyses to relate ten traits hypothesized to affect assemblage structure with the “role” of each species in the scavenging assemblage in which it appeared. We characterized the role of a species in terms of both the proportion of monitored carcasses on which that species scavenged, or scavenging breadth (i.e., the species “normalized degree”), and the role of that species in the nested structure of the assemblage (i.e., the species “paired nested degree”), therefore identifying possible facilitative interactions among species. We found that species with high olfactory acuity, social foragers, and obligate scavengers had the widest scavenging breadth. We also found that social foragers had a large paired nested degree in scavenger assemblages, probably because their presence is easier to detect by other species to signal carcass occurrence. Our study highlights differences in the functional roles of scavenger species and can be used to identify key species for targeted conservation to maintain the ecological function of scavenger assemblages.
54 ENVIRONMENTAL SCIENCES↗