WaTEM/SEDEM's capability in simulating watershed-scale soil conservation: using the GLUE approach to analyse the representation of in-field processes and connectivity features along thalwegs [Abstract]

Testing the performance of soil erosion models against observational data is a critical step in any model application. This is particularly important when models aid land-management decisions, e.g. planning and implementing soil conservation practices in agricultural landscapes. However, observational erosion data are uncertain and typically restricted to measurements of sediment fluxes at the outlet of a system, e.g. plot or watershed. This has limited utility for testing a model’s representation of landscape sediment connectivity processes, which is crucial for planning soil conservation and off-site pollution control measures. Here, the performance of a Python-implemented version of the spatially distributed soil erosion and sediment yield WaTEM/SEDEM model was evaluated for simulating sediment yields under soil conservation conditions across contrasting watersheds at an experimental farm in Southern Germany. To do so, we used an eight-year monitoring dataset (1994-2001) that includes high-resolution measurements of soil properties, plant traits, and land management operations, as well as event-based sediment yield measurements for (I) four small-scale watersheds (0.8 to 4.2 ha) primarily representing in-field erosion processes (mostly supply-limited) and (II) two cascading watersheds (5.7 to 7.8 ha) dominated by sedimentation processes along a grassed waterway (mostly transport-limited). Further, we employed a Generalised Likelihood Uncertainty Estimation (GLUE) rejectionist framework utilising Monte Carlo simulations with 25,000 iterations to condition model parameters. The model performance was evaluated across two spatial scales - from individual watersheds to aggregated supply-limited and transport-limited watershed groups - and temporal scales ranging from single-year to eight-year averages. Model iterations were considered as behavioural when their simulated sediment yields fell within an estimated error range derived from the monitoring dataset. The model demonstrated capability in simulating low sediment yields when aggregated spatially and temporally. However, the annual-scale model applications were rejected due to insufficient representation of temporal dynamics. The results indicated a systematic overestimation of sediment yields across most watersheds, with a notable exception in one transport-limited catchment where underestimation occurred. The influence of retention features within watersheds was reflected by the behavioural parameter selection: in cases of sediment yield overestimation, parameters enhancing deposition produced superior results, while in watersheds with underestimated sediment yields, parameters reducing deposition improved model performance. These observations underscore the model's capability to represent low sediment yields in agricultural landscapes under soil conservation while highlighting temporal resolution limitations and the importance of comprehensive uncertainty analysis in measured and simulated data

Evolution of vacuolar proton pyrophosphatase domains and volutin granules: clues into the early evolutionary origin of the acidocalcisome

Background: Volutin granules appear to be universally distributed and are morphologically and chemically identical to acidocalcisomes, which are electron-dense granular organelles rich in calcium and phosphate, whose functions include storage of phosphorus and various metal ions, metabolism of polyphosphate, maintenance of intracellular pH, osmoregulation and calcium homeostasis. Prokaryotes are thought to differ from eukaryotes in that they lack membrane-bounded organelles. However, it has been demonstrated that as in acidocalcisomes, the calcium and polyphosphate-rich intracellular "volutin granules (polyphosphate bodies)" in two bacterial species, Agrobacterium tumefaciens, and Rhodospirillum rubrum, are membrane bound and that the vacuolar proton-translocating pyrophosphatases (V-H+PPases) are present in their surrounding membranes. Volutin granules and acidocalcisomes have been found in organisms as diverse as bacteria and humans.Results: Here, we show volutin granules also occur in Archaea and are, therefore, present in the three superkingdoms of life (Archaea, Bacteria and Eukarya). Molecular analyses of V-H+PPase pumps, which acidify the acidocalcisome lumen and are diagnostic proteins of the organelle, also reveal the presence of this enzyme in all three superkingdoms suggesting it is ancient and universal. Since V-H+PPase sequences contained limited phylogenetic signal to fully resolve the ancestral nodes of the tree, we investigated the divergence of protein domains in the V-H+PPase molecules. Using Protein family (Pfam) database, we found a domain in the protein, PF03030. The domain is shared by 31 species in Eukarya, 231 in Bacteria, and 17 in Archaea. The universal distribution of the V-H+PPase PF03030 domain, which is associated with the V-H+PPase function, suggests the domain and the enzyme were already present in the Last Universal Common Ancestor (LUCA).Conclusion: The importance of the V-H+PPase function and the evolutionary dynamics of these domains support the early origin of the acidocalcisome organelle. In particular, the universality of volutin granules and presence of a functional V-H+PPase domain in the three superkingdoms of life reveals that the acidocalcisomes may have appeared earlier than the divergence of the superkingdoms. This result is remarkable and highlights the possibility that a high degree of cellular compartmentalization could already have been present in the LUCA.Reviewers: This article was reviewed by Anthony Poole, Lakshminarayan Iyer and Daniel Kahn.open

The maize ALDH protein superfamily: linking structural features to functional specificities

<p>Abstract</p> <p>Background</p> <p>The completion of maize genome sequencing has resulted in the identification of a large number of uncharacterized genes. Gene annotation and functional characterization of gene products are important to uncover novel protein functionality.</p> <p>Results</p> <p>In this paper, we identify, and annotate members of all the maize aldehyde dehydrogenase (ALDH) gene superfamily according to the revised nomenclature criteria developed by ALDH Gene Nomenclature Committee (AGNC). The maize genome contains 24 unique <it>ALDH </it>sequences encoding members of ten ALDH protein families including the previously identified male fertility restoration <it>RF2A </it>gene, which encodes a member of mitochondrial class 2 ALDHs. Using computational modeling analysis we report here the identification, the physico-chemical properties, and the amino acid residue analysis of a novel tunnel like cavity exclusively found in the maize sterility restorer protein, RF2A/ALDH2B2 by which this protein is suggested to bind variably long chain molecular ligands and/or potentially harmful molecules.</p> <p>Conclusions</p> <p>Our finding indicates that maize ALDH superfamily is the most expanded of plant <it>ALDHs </it>ever characterized, and the mitochondrial maize RF2A/ALDH2B2 is the only plant ALDH that harbors a newly defined pocket/cavity with suggested functional specificity.</p

Gut bacteria facilitate adaptation to crop rotation in the western corn rootworm

11917-11922Insects are constantly adapting to human-driven landscape changes; however, the roles of their gut microbiota in these processes remain largely unknown. The western corn rootworm (WCR, Diabrotica virgifera virgifera LeConte) (Coleoptera: Chrysomelidae) is amajor corn pest that has been controlled via annual rotation between corn (Zea mays) and nonhost soybean (Glycine max) in the United States. This practice selected for a 'rotation-resistant' variant (RR-WCR) with reduced ovipositional fidelity to cornfields.When in soybean fields, RRWCRs also exhibit an elevated tolerance of antiherbivory defenses (i.e., cysteine protease inhibitors) expressed in soybean foliage. Here we show that gut bacterial microbiota is an important factor facilitating this corn specialist's (WCR's) physiological adaptation to brief soybean herbivory. Comparisons of gut microbiota between RR- and wild-type WCR (WT-WCR) revealed concomitant shifts in bacterial community structure with host adaptation to soybean diets. Antibiotic suppression of gut bacteria significantly reduced RR-WCR tolerance of soybean herbivory to the level of WT-WCR, whereas WTWCR were unaffected. Our findings demonstrate that gut bacteria help to facilitate rapid adaptation of insects inmanaged ecosystems

Erosion-SAM: Semantic segmentation of soil erosion by water

Soil erosion (SE) by water threatens global agriculture by depleting fertile topsoil and causing economic costs. Conventional SE models struggle to capture the complex, non-linear interactions between SE drivers. Recently, machine learning has gained attention for SE modeling. However, machine learning requires large data sets for effective training and validation. In this study, we present Erosion-SAM, which fine-tunes the Segment Anything Model (SAM) for automatic segmentation of water erosion features in high-resolution remote sensing imagery. The data set comprised 405 manually segmented agricultural fields from erosion-prone areas obtained from the rain gauge-adjusted radar rainfall data (RADOLAN) for bare cropland, vegetated cropland, and grassland. Three approaches were evaluated: two pre-processing techniques— resizing and cropping — and an improved version of the resizing approach with user-defined prompts during the testing phase. All fine-tuned models outperformed the original SAM, with the prompt-based resizing method showing the highest accuracy, especially for grassland (recall: 0.90, precision: 0.82, dice coefficient: 0.86, IoU: 0.75). SAM performed better than the cropping approach only on bare cropland. This discrepancy is attributed to the tendency of SAM to overestimate SE by classifying a large proportion of fields as eroded, which increases recall by covering most of the eroded pixels. All three fine-tuned approaches showed strong correlations with the actual SE severity ratios, with the prompt-enhanced resizing approach achieving the highest R2 of 0.93. In summary, Erosion-SAM shows promising potential for automatically detecting SE features from remote sensing images. The generated data sets can be applied to machine learning-based SE modeling, providing accurate and consistent training data across different land cover types, and offering a reliable alternative to traditional SE models. In addition, erosion-SAM can make a valuable contribution to the precise monitoring of SE with high temporal resolution over large areas, and its results could benefit reinsurance and insurance-related risk solutions

Varieties of living things: Life at the intersection of lineage and metabolism

publication-status: Publishedtypes: Articl

Patterns of differential gene expression in adult rotation - resistant and wild - type western corn rootworm digestive tracts

692-704The western corn rootworm (WCR, Diabrotica virgifera virgifera LeConte) is an important pest of corn. Annual crop rotation between corn and soybean disrupts the corn-dependent WCR life cycle and is widely adopted to manage this pest. This strategy selected for rotation-resistant (RR) WCR with reduced ovipositional fidelity to corn. Previous studies revealed that RR-WCR adults exhibit greater tolerance of soybean diets, different gut physiology, and host-microbe interactions compared to rotation-susceptible wild types (WT). To identify the genetic mechanisms underlying these phenotypic changes, a de novo assembly of the WCR adult gut transcriptome was constructed and used for RNA-sequencing analyses of RNA libraries from different WCR phenotypes fed with corn or soybean diets. Global gene expression profiles of WT- and RR-WCR were similar when feeding on corn diets, but different when feeding on soybean. Using network- based methods, we identified gene modules transcriptionally correlated with the RR phenotype. Gene ontology enrichment analyses indicated that the functions of these modules were related to metabolic processes, immune responses, biological adhesion, and other functions/processes that appear to correlate to documented traits in RR populations. These results suggest that gut transcriptomic divergence correlated with brief soybean feeding and other physiological traits may exist between RR- and WT-WCR adults

Mitochondrial Genome Sequence and Expression Profiling for the Legume Pod Borer Maruca vitrata (Lepidoptera: Crambidae)

We report the assembly of the 14,054 bp near complete sequencing of the mitochondrial genome of the legume pod borer (LPB), Maruca vitrata (Lepidoptera: Crambidae), which we subsequently used to estimate divergence and relationships within the lepidopteran lineage. The arrangement and orientation of the 13 protein-coding, 2 rRNA, and 19 tRNA genes sequenced was typical of insect mitochondrial DNA sequences described to date. The sequence contained a high A+T content of 80.1% and a bias for the use of codons with A or T nucleotides in the 3rd position. Transcript mapping with midgut and salivary gland ESTs for mitochondrial genome annotation showed that translation from protein-coding genes initiates and terminates at standard mitochondrial codons, except for the coxI gene, which may start from an arginine CGA codon. The genomic copy of coxII terminates at a T nucleotide, and a proposed polyadenylation mechanism for completion of the TAA stop codon was confirmed by comparisons to EST data. EST contig data further showed that mature M. vitrata mitochondrial transcripts are monocistronic, except for bicistronic transcripts for overlapping genes nd4/nd4L and nd6/cytb, and a tricistronic transcript for atp8/atp6/coxIII. This processing of polycistronic mitochondrial transcripts adheres to the tRNA punctuated cleavage mechanism, whereby mature transcripts are cleaved only at intervening tRNA gene sequences. In contrast, the tricistronic atp8/atp6/coxIII in Drosophila is present as separate atp8/atp6 and coxIII transcripts despite the lack of an intervening tRNA. Our results indicate that mitochondrial processing mechanisms vary between arthropod species, and that it is crucial to use transcriptional information to obtain full annotation of mitochondrial genomes

Calcium- and polyphosphate-containing acidic granules of sea urchin eggs are similar to acidocalcisomes, but are not the targets for NAADP

Acidocalcisomes are acidic calcium-storage compartments described from bacteria to humans and characterized by their high content in poly P (polyphosphate), a linear polymer of many tens to hundreds of Pi residues linked by high-energy phosphoanhydride bonds. In the present paper we report that millimolar levels of short-chain poly P (in terms of Pi residues) and inorganic PPi are present in sea urchin extracts as detected using 31P-NMR, enzymatic determinations and agarose gel electrophoresis. Poly P was localized to granules randomly distributed in the sea urchin eggs, as shown by labelling with the poly-P-binding domain of Escherichia coli exopolyphosphatase. These granules were enriched using iodixanol centrifugation and shown to be acidic and to contain poly P, as determined by Acridine Orange and DAPI (4′,6′-diamidino-2-phenylindole) staining respectively. These granules also contained large amounts of calcium, sodium, magnesium, potassium and zinc, as detected by X-ray microanalysis, and bafilomycin A1-sensitive ATPase, pyrophosphatase and exopolyphosphatase activities, as well as Ca2+/H+ and Na+/H+ exchange activities, being therefore similar to acidocalcisomes described in other organisms. Calcium release from these granules induced by nigericin was associated with poly P hydrolysis. Although NAADP (nicotinic acid–adenine dinucleotide phosphate) released calcium from the granule fraction, this activity was not significantly enriched as compared with the NAADP-stimulated calcium release from homogenates and was not accompanied by poly P hydrolysis. GPN (glycyl-L-phenylalanine-naphthylamide) released calcium when added to sea urchin homogenates, but was unable to release calcium from acidocalcisome-enriched fractions, suggesting that these acidic stores are not the targets for NAADP

Variation in Arabidopsis Flowering Time Associated with Cis-Regulatory Variation in CONSTANS

The onset of flowering, the change from vegetative to reproductive development, is a major life history transition in flowering plants. Recent work suggests that mutations in cis-regulatory mutations should play critical roles in the evolution of this (as well as other) important adaptive traits, but thus far there has been little evidence that directly links regulatory mutations to evolutionary change at the species level. While several genes have previously been shown to affect natural variation in flowering time in Arabidopsis thaliana, most either show protein-coding changes and/or are found at low frequency (\u3c5%). Here we identify and characterize natural variation in the cis-regulatory sequence in the transcription factor CONSTANS that underlies flowering time diversity in Arabidopsis. Mutation in this regulatory motif evolved recently and has spread to high frequency in Arabidopsis natural accessions, suggesting a role for these cis-regulatory changes in adaptive variation of flowering time