The timing of flowering, and in particular the degree to which it is responsive to the environment, is a key factor in the adaptation of a given species to various eco-geographic locations and ...agricultural practices. Flowering time variation has been documented in many crop legumes, and selection for specific variants has permitted significant expansion and improvement in cultivation, from prehistoric times to the present day. Recent advances in legume genomics have accelerated the process of gene identification and functional analysis, and opened up new prospects for a molecular understanding of flowering time adaptation in this important crop group. Within the legumes, two species have been prominent in flowering time studies; the vernalization-responsive long-day species pea (Pisum sativum) and the warm-season short-day plant soybean (Glycine max). Analysis of flowering in these species is now being complemented by reverse genetics capabilities in the model legumes Medicago truncatula and Lotus japonicus, and the emergence of genome-scale resources in a range of other legumes. This review will outline the insights gained from detailed forward genetic analysis of flowering time in pea and soybean, highlighting the importance of light perception, the circadian clock and the FT family of flowering integrators. It discusses the current state of knowledge on genetic mechanisms for photoperiod and vernalization response, and concludes with a broader discussion of flowering time adaptation across legumes generally.
One strategy for restoring degraded soils by opencast mining in semiarid regions is the application of organic amendments. However, selecting an appropriate organic amendment that improves soil ...quality and functionality for recovery in the short-term without a high contribution to increased CO₂ emissions is important for improving restoration strategies. Therefore, the objective of this work was to study the short and medium-term changes in physico-chemical and biological properties in restored soils with organic amendments from a limestone quarry (SE, Spain). Several restoration treatments were applied consisting stabilized sewage sludge, vegetable compost garden waste, vegetable compost from greenhouse crop residues and two mixtures thereof, then native plants were planted. After six months several soil properties were evaluated (electrical conductivity (EC), pH, total organic carbon (TOC), total nitrogen (TN), assimilable phosphorus (AP), soil water retention, carbohydrates and polyphenols content, enzymatic activities, bacteria and fungi fatty acids and soil respiration). Some physico-chemical soil properties and the survival rates and biovolume of the introduced native plants, as well as the percentage of land cover occupied by wild plants, were also analyzed 2 years after the application of the amendments. Organic amendments improved significantly all soil properties compared with unamended soils. Labile organic matter forms (carbohydrates and polyphenols) showed significant positive correlations with parameters related to microbial activity. Restored soils with sewage sludge had the highest significant labile C values, following by its mixtures. All organic amendments increased in situ CO₂ release, a positive priming effect and organic matter mineralization, being these properties higher in sludge-treated soils than in the rest restored and non-amendment soils. The content of TOC and TN and water retention remained similar two after the application of the amendments, but the EC decreased in restored soils. Nevertheless, despite PCA analysis clearly demonstrated that all restoration treatments had an important effect on the functionality and soil quality, vegetable compost from garden waste or from horticultural greenhouse crop waste amendments were the best restoration treatments for short and medium-term restoration of degraded quarry soils in harsh environmental and climate conditions because they also presented lower CO2 emission rates to the atmosphere and the highest survival and growth rates of the introduced plants and wild cover in the experimental plots.
•Organic amendments modify the physico-chemical properties in restored soil•Labile fraction of carbon stimulates the bacterial biomass and enzyme activities•Organic amendments increase soil quality and soil functionality•Organic amendments promote positive priming effect after application•High content of labile organic matter in organic amendment increased CO₂ emissions
Drylands are areas under continuous degradation and desertification frequently covered by cyanobacterial biocrusts. Several studies have indicated that soil microorganisms contribute to nutrient ...cycling. Nevertheless, little is still known about how those could potentially be participating according to their taxonomic groups. In addition, biocrust-associated communities still remain largely unexplored at taxonomic and functional levels and, therefore, biotechnologically underexploited in comparison with other terrestrial ecosystems. This work aimed at revealing the ecological and biotechnological potential of soil communities using a shotgun sequencing approach in cyanobacterial-colonised biocrusts in the Tabernas Desert regarding the cycles of carbon, nitrogen, phosphorus, iron, sulfur, and potassium. The abundance and successful adaptation of major groups Rubrobacter and Conexibacter was explained by the presence of metabolic diversity regarding glycolytic and CO2 fixation pathways but also by exhibiting a rich pool of hydrolytic enzymes. Besides, Rubrobacter representatives might potentially be driving sulfate mineralisation. Others, such as Caulobacter representatives, were also suggested to have a potential key role in K+ uptake. Furthermore, iron uptake was found to potentially be mediated via synthesis and release of siderophores, mostly derived from pseudomonads. Importantly, this work revealed a meaningful biotechnological niche in which the recovery of novel isolates is a very desirable step forward for the industry and a step forward in unwrapping the potential role of those microorganisms in soil restoration as well as in the functioning of arid soils as CO2 sinks.
•Rubrobacter and Conexibacter members present a rich pool of hydrolytic enzymes.•Major groups Rubrobacter and Conexibacter exhibit Calvon-Benson-Basshan cycle.•Rubrobacter representatives might be driving sulfate mineralisation.•Caulobacter representatives are suggested to have a potential key role in K+ uptake.•Conexibacter, Rubrobacter and Caulobacter isolates would be desirable for industry.
Biocrusts are an essential soil surface cover at drylands where ecosystems are especially fragile to soil degradation processes due to climatic peculiarities. In the present work, (micro)biological ...and physicochemical properties indicative of soil functionality were studied in two different biocrust types dominated by Dipolschistes diacapsis and Lepraria isidiata and in underlying soil at two different depths (SL1, soil layer right below the biocrusts, and SL2, soil layer underlying SL1) at the Tabernas desert (southeast Spain). The influence of climatic factors (rainfall and temperature) and general soil properties on the (micro)biological properties were also analyzed in different environmental (climatic) conditions over a period of two years. PERMANOVA analyses showed significant statistical differences (Pseudo-F = 63.9; P (perm) = 0.001) among biocrust and soil layers. Throughout the study period, enzyme activities involved in C, N, and P cycles; microbial biomass-C; basal respiration; and several properties directly related to ecosystem productivity (total organic carbon, total nitrogen, concentration of ammonium and nitrate) were higher in both biocrust types than in the underlying soil layers, showing that biocrusts improved soil functions related to nutrient cycling. These properties progressively diminished in successive soil layers under the biocrusts (biocrusts > SL1 > SL2). Biocrusts showed greater similarity to each other and to SL1 than to SL2 in (micro)biological properties. A distance-based linear model analysis showed that total organic carbon, rainfall, pH, mineralized N-NH4+, and total nitrogen were the most important variables for predicting (micro)biological soil properties in biocrusts. Different biochemical behavior between the biocrusts and successive underlying soil layers has been found in wet periods. After rainfall periods, the biocrusts showed important peaks in basal soil respiration and in enzyme activities involved in C and P cycles. Nevertheless, soil biochemical properties hardly showed any peak in SL1 and did not change in SL2 despite soil moisture being higher in the soil layers below the biocrusts. Correlation analyses corroborated the existence of different relationships between soil moisture and enzymatic activities. In biocrusts, soil moisture showed a greater number of significant positive correlations with enzymes such as β-glucosidase, invertase, and phosphomonoesterase among others, whereas in SL1 it was only correlated with cellulase and in SL2 with dehydrogenase. A change in rainfall regime, as predicted by models based on climate change in arid and semiarid zones, could affect the activity of soil enzymes in the biocrusts and underlying layers, thus aggravating the degradation of these fragile dryland ecosystems.
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•Rainfall in drylands modifies the functional response of biocrusts and underlying soil.•Biocrusts affect N and C cycling and modulate response to seasonal climatic conditions.•The extent of biocrusts response to rainfall events varied with the dominant lichen.•Biocrust-induced changes in soil physicochemical factors affect soil microbial activity.•Biocrusts showed higher functionality than the underlying soil layers.
Summary
Legumes usually have compound inflorescences, where flowers/pods develop from secondary inflorescences (I2), formed laterally at the primary inflorescence (I1). Number of flowers per I2, ...characteristic of each legume species, has important ecological and evolutionary relevance as it determines diversity in inflorescence architecture; moreover, it is also agronomically important for its potential impact on yield. Nevertheless, the genetic network controlling the number of flowers per I2 is virtually unknown.
Chickpea (Cicer arietinum) typically produces one flower per I2 but single flower (sfl) mutants produce two (double‐pod phenotype). We isolated the SFL gene by mapping the sfl‐d mutation and identifying and characterising a second mutant allele. We analysed the effect of sfl on chickpea inflorescence ontogeny with scanning electron microscopy and studied the expression of SFL and meristem identity genes by RNA in situ hybridisation.
We show that SFL corresponds to CaRAX1/2a, which codes a MYB transcription factor specifically expressed in the I2 meristem.
Our findings reveal SFL as a central factor controlling chickpea inflorescence architecture, acting in the I2 meristem to regulate the length of the period for which it remains active, and therefore determining the number of floral meristems that it can produce.
Digital evolution is a branch of artificial life in which self-replicating computer programs—digital organisms—mutate and evolve within a user-defined computational environment. In spite of its value ...in biology, we still lack an up-to-date and comprehensive database on digital organisms resulting from evolution experiments. Therefore, we have developed an ontology-based semantic database—avidaDB—and an R package—avidaR—that provides users of the R programming language with an easy-to-use tool for performing complex queries without specific knowledge of SPARQL or RDF. avidaR can be used to do research on robustness, evolvability, complexity, phenotypic plasticity, gene regulatory networks, and genomic architecture by retrieving the genomes, phenotypes, and transcriptomes of more than a million digital organisms available on avidaDB. avidaR is already accepted on CRAN (
i.e.
, a comprehensive collection of R packages contributed by the R community) and will make biologists better equipped to embrace the field of digital evolution.
Humanity has undertaken actions to decarbonize the main CO2-emitting industries, such as the energy industry. The solution to this problem has been to use renewable energy sources, with positive ...results in recent years. The objective of the present research was to analyze the scientific advances produced in research on renewable energy and energy production globally during the years 2019 and 2023. The purpose was to determine the current status and future trends in renewable energies in order to contribute to the scientific community by identifying potential risks and encouraging collaboration between authors, institutions, and countries. A bibliometric analysis was performed in the Scopus database using the keywords “renewable energies” and “energy production” within a search equation with a time limit of 2019 and 2023. Keyword co-occurrence and collaboration between authors and countries were performed with VOS Viewer software. It was determined, using per capita research analysis, that the leaders in this research were Cyprus, Denmark, Qatar, Norway, and Ireland. The leading institutions in this field of research are the Technical University of Denmark; Aalborg University; and the Ministry of Education, China. The predominant research topics were energy, engineering, and environmental sciences, related to energy sources such as biomass, hydrogen, or wave energy. The results described here have the potential to contribute to the scientific community, stimulating new research and identifying new needs in the existing literature.
Microplastics (MPs) are a significant threat to soils. However, there is scarce information on the impact of MPs on soil properties, particularly in volcanic ash‐derived soils. The objective of this ...study was to evaluate the impact of polyamide (PA) and low‐density polyethylene (LDPE) MPs on the biological and chemical characteristics of an Andisol from central Chile. Twenty‐one parameters were evaluated, including pH, electrical conductivity (EC), total organic carbon (TOC), dissolved organic carbon (DOC), total phosphorus (TP), available phosphorous (AP), available nitrogen (AN), inorganic nitrogen forms (NH4+, NO2− and NO3), carbohydrates (CHO), polyphenols (POLs), humic substances, soil basal respiration (SBR) and activities of soil enzymes such as dehydrogenase, β‐glucosidase, phosphatase and urease. For this, a microcosm was set up in clay pots in an incubation chamber at 21°C and 60% soil moisture, with the addition of PA and LDPE at doses of 1% and 3% w/w; a control treatment consisting of microcosm without MPs was also included. After 6 weeks of incubation, PA addition resulted in an increase in TOC and NH4+ by up to 32% and 26%, respectively, and a decrease in NO3− by 22%. AP decreased by 15%–19% with the addition of PA and LDPE. Similarly, acid phosphatase and β‐glucosidase activities decreased by 15% and 26% with PA and LDPE, respectively. The distance‐based linear model (DistLM) was used to analyse relationships in chemical and biological datasets. The analysis revealed that TOC and TP were primary components in the best model for predicting microbiological changes (R2 = .469, AICs = 16.026), indicating that MPs accumulation affects soil carbon cycling and P content. Overall, the results show that MPs addition alters soil chemical and microbiological properties in Andisols, with varying effects depending on the type and dose of MPs, with the highest dose (3%) producing the most marked negative effects.
Abstract
The Ontology for Avida (OntoAvida) aims to develop an integrated vocabulary for the description of Avida, the most widely used computational approach for performing experimental evolution ...using digital organisms–self-replicating computer programs that evolve within a user-defined computational environment. The lack of a clearly defined vocabulary makes some biologists feel reluctant to embrace the field of digital evolution. This integrated framework empowers biologists by equipping them with the necessary tools to explore and analyze the field of digital evolution more effectively. By leveraging the vocabulary of Avida, researchers can gain deeper insights into the evolutionary processes and dynamics of digital organisms. In addition, OntoAvida allows researchers to make inference based on certain rules and constraints, facilitate the reproducibility of
in silico
evolution experiments and trace the provenance of the data stored in avidaDB–an RDF database containing the genomes, transcriptomes, and phenotypes of more than a million digital organisms. OntoAvida is part of the Open Biological and Biomedical Ontologies (OBO Foundry) and is available at
http://www.obofoundry.org/ontology/ontoavida.html
.
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