Hierarchies, integration and complexity in biology: a possible framework for evo-devo

Históricamente, las jerarquías han servido para clasificar y organizar la vida. Actualmente, es claro que capturar conceptualmente la complejidad y diversidad de la vida, requiere más de una sola jerarquía. Aquí se abordan algunos de los principales retos que enfrentan las jerarquías al procurar aprehender la biodiversidad. Para resolverlos, se propone una red de jerarquías que sirven de descriptores de procesos con genidentidad y pluralismo ontológico, desde una perspectiva y nivel particulares. La red de jerarquías se concibe como un conjunto de ramas en crecimiento que pueden dividirse y unirse de múltiples maneras. Nuestra perspectiva resuelve varios de los problemas identificados e integra perspectivas multinivel justo lo que se requiere para construir del marco demandado por la evo-devo.Throughout history hierarchies have been useful for categorizing and organizing life. It is clear that one hierarchy is not enough for the conceptualization of the complexity and diversity of life as we currently understand them. In this paper we address some of the key challenges associated hierarchies when apprehending biodiversity. Furthermore, we propose a network which consists of different hierarchies that serve as descriptors of processes with genidentity and ontological pluralism. Each hierarchy describes a process from a particular perspective and level. Thus, this network is conceived as growing branches that can divide and join multiple ways. Our approach solves several of the identified challenges and it becomes a way of integrating thoughts to allow the construction of a framework required by evo-devo.Fil: Casanueva, Mario. Universidad Autónoma Metropolitana; MéxicoFil: Folguera, Guillermo. Universidad de Buenos Aires. Facultad de Filosofía y Letras; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Peimbert, Mariana. Universidad Autónoma Metropolitana; Méxic

Jerarquías, integración y complejidad en biología. Un posible marco para la evo-devo

RESUMENHistóricamente, las jerarquías han servido para clasificar y organizar la vida. Actualmente, es claro que capturar conceptualmente la complejidad y diversidad de la vida, requiere más de una sola jerarquía. Aquí se abordan algunos de los principales retos que enfrentan las jerarquías al procurar aprehender la biodiversidad. Para resolverlos, se propone una red de jerarquías que sirven de descriptores de procesos con genidentidad y pluralismo ontológico, desde una perspectiva y nivel particulares. La red de jerarquías se concibe como un conjunto de ramas en crecimiento que pueden dividirse y unirse de múltiples maneras. Nuestra perspectiva resuelve varios de los problemas identificados e integra perspectivas multinivel justo lo que se requiere para construir del marco demandado por la evo-devo.PALABRAS CLAVEEVO-DEVO, DIVERSIDAD BIOLÓGICA, PLURALISMO ONTOLÓGICO, TIEMPO EN BIOLOGÍA, TEORÍAS MULTINIVELABSTRACTThroughout history hierarchies have been useful for categorizing and organizing life. It is clear that one hierarchy is not enough for the conceptualization of the complexity and diversity of life as we currently understand them. In this paper we address some of the key challenges associated hierarchies when apprehending biodiversity. Furthermore, we propose a network which consists of different hierarchies that serve as descriptors of processes with genidentity and ontological pluralism. Each hierarchy describes a process from a particular perspective and level. Thus, this network is conceived as growing branches that can divide and join multiple ways. Our approach solves several of the identified challenges and it becomes a way of integrating thoughts to allow the construction of a framework required by evo-devo.KEY WORDSEVO-DEVO, DIVERSITY OF LIFE, ONTOLOGICAL PLURALISM, TIME IN BIOLOGY, MULTI-LEVEL THEORIE

Degradation of a benzene–toluene mixture by hydrocarbon-adapted bacterial communities

We examined the rate of degradation of a benzene–toluene mixture in aerobic microcosms prepared with samples of an aquifer that lies below a petrochemical plant (SIReN, UK). Five samples exposed to different concentrations of benzene (from 0.6 to 317 mg l−1) were used. Fast degradation (approx. 1–6 mg l−1 day−1) of both contaminants was observed in all groundwater samples and complete degradation was recorded by the seventh day except for one sample. We also identified the microbial community in each of the samples by culture-independent techniques. Two of the less impacted samples harbour the aerobic benzene degrader Pseudomonas fluorescens, while Acidovorax and Arthrobacter spp. were found in the most polluted sample and are consistent with the population observed in situ. Hydrogenophaga was found in the deepest sample while Rhodoferax spp. were recovered in an alkaline sample (pH 8.4) and may also be implicated in benzene degradation. Time series analysis shows that each of the samples has a different community but they remain stable over the degradation period. This study provides new information on a well not previously studied (no. 309s) and confirms that adapted communities have the ability to degrade hydrocarbon mixtures and could be used in further bioaugmentation approaches in contaminated sites

Fileset: Exploring the cockatiel (Nymphicus hollandicus) fecal microbiome, bacterial inhabitants of a worldwide pet

OTU tables in biom and tabular format, taxa profiles, and bioinformatic protocols used for the manuscript: <br><br><p> </p><p><b>Exploring the cockatiel (</b><i><b>Nymphicus hollandicus</b></i><b>) fecal microbiome, bacterial inhabitants of a worldwide pet</b></p><br><p>Authors: Luis David Alcaraz^a, Apolinar M. Hernández^b, and Mariana Peimbert^b,*</p><p>^aLaboratorio Nacional de Ciencias de la Sostenibilidad. Instituto de Ecología. Universidad Nacional Autónoma de México. AP 70-275, Ciudad Universitaria, UNAM, 04510, Cd. Mx., México.</p><p>^b Departamento de Ciencias Naturales. Universidad Autónoma Metropolitana, Unidad Cuajimalpa. Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, 05348, Cd. Mx., México. </p><br><p>Corresponding author</p><p>Mariana Peimbert</p><p>E-mail address: <a href="mailto:[email protected]">[email protected]</a> </p><p>Tel.: (5255) 5814 6500 ext. 3878</p><br

A study of microbial diversity in a biofertilizer consortium.

Biofertilizers supply living microorganisms to help plants grow and keep their health. This study examines the microbiome composition of a commercial biofertilizer known for its plant growth-promoting activity. Using ITS and 16S rRNA gene sequence analyses, we describe the microbial communities of a biofertilizer, with 163 fungal species and 485 bacterial genera found. The biofertilizer contains a variety of microorganisms previously reported to enhance nutrient uptake, phytohormone production, stress tolerance, and pathogen resistance in plants. Plant roots created a microenvironment that boosted bacterial diversity but filtered fungal communities. Notably, preserving the fungal-inoculated substrate proves critical for keeping fungal diversity in the root fraction. We described that bacteria were more diverse in the rhizosphere than in the substrate. In contrast, root-associated fungi were less diverse than the substrate ones. We propose using plant roots as bioreactors to sustain dynamic environments that promote the proliferation of microorganisms with biofertilizer potential. The study suggests that bacteria grow close to plant roots, while root-associated fungi may be a subset of the substrate fungi. These findings show that the composition of the biofertilizer may be influenced by the selection of microorganisms associated with plant roots, which could have implications for the effectiveness of the biofertilizer in promoting plant growth. In conclusion, our study sheds light on the intricate interplay between plant roots and the biofertilizer's microbial communities. Understanding this relationship can aid in optimizing biofertilizer production and application, contributing to sustainable agricultural practices and improved crop yields

Passenger-surface microbiome interactions in the subway of Mexico City.

Interaction between hands and the environment permits the interchange of microorganisms. The Mexico City subway is used daily by millions of passengers that get in contact with its surfaces. In this study, we used 16S rRNA gene sequencing to characterize the microbiomes of frequently touched surfaces and compare regular and women-only wagons. We also explored the effect of surface cleaning on microbial resettling. Finally, we studied passenger behavior and characterized microbial changes after traveling. Most passengers (99%), showed some type of surface interaction during a wagon trip, mostly with the hands (92%). We found microbiome differences associated with surfaces, probably reflecting diverse surface materials and usage frequency. The platform floor was the most bacterial diverse surface, while the stair handrail and pole were the least diverse ones. After pole cleaning, the resettling of microbial diversity was fast (5-30 minutes); however, it did not resemble the initial composition. After traveling, passengers significantly increased their hand microbial diversity and converged to a similar microbial composition among passengers. Additionally, passenger hand microbiomes resembled subway surfaces in diversity. However, microbial fingerprints were preserved within passengers after traveling

<i>Wolbachia</i> diversity in mosquito microbiomes.

A) Neighbor-joining tree of the Wolbachia 16S rRNA gene OTUs. Rickettsia canadensis, Gordonia lacunae, and Salmonella enterica were used as outgroups. OTUs from Supergroup A are highlighted in blue, while Supergroup B is highlighted in yellow. B) UpSet diagram of the distribution of Wolbachia shared OTUs.</p

Supplementary figures and tables.

The mosquito Aedes spp. holds important relevance for human and animal health, as it serves as a vector for transmitting multiple diseases, including dengue and Zika virus. The microbiome’s impact on its host’s health and fitness is well known. However, most studies on mosquito microbiomes have been conducted in laboratory settings. We explored the mixed microbial communities within Aedes spp., utilizing the 16S rRNA gene for diversity analysis and shotgun metagenomics for functional genomics. Our samples, which included Ae. aegypti and Ae. albopictus, spanned various developmental stages—eggs, larvae, and adults—gathered from five semiurban areas in Mexico. Our findings revealed a substantial diversity of 8,346 operational taxonomic units (OTUs), representing 967 bacterial genera and 126,366 annotated proteins. The host developmental stage was identified as the primary factor associated with variations in the microbiome composition. Subsequently, we searched for genes and species involved in mosquito biocontrol. Wolbachia accounted for 9.6% of the 16S gene sequences. We observed a high diversity (203 OTUs) of Wolbachia strains commonly associated with mosquitoes, such as wAlb, with a noticeable increase in abundance during the adult stages. Notably, we detected the presence of the cifA and cifB genes, which are associated with Wolbachia’s cytoplasmic incompatibility, a biocontrol mechanism. Additionally, we identified 221 OTUs related to Bacillus, including strains linked to B. thuringiensis. Furthermore, we discovered multiple genes encoding insecticidal toxins, such as Cry, Mcf, Vip, and Vpp. Overall, our study contributes to the understanding of mosquito microbiome biodiversity and metabolic capabilities, which are essential for developing effective biocontrol strategies against this disease vector.</div