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NAC proteins constitute one of the largest groups of plant-specific transcription factors and are known to play essential roles in various developmental processes. They are also important in plant responses to stresses such as drought, soil salinity, cold, and heat, which adversely affect growth. The current knowledge regarding the distribution of NAC proteins in plant lineages comes from relatively small samplings from the available data. In the present study, we broadened the number of plant species containing the NAC family origin and evolution to shed new light on the evolutionary history of this family in angiosperms. A comparative genome analysis was performed on 24 land plant species, and NAC ortholog groups were identified by means of bidirectional BLAST hits. Large NAC gene families are found in those species that have experienced more whole-genome duplication events, pointing to an expansion of the NAC family with divergent functions in flowering plants. A total of 3,187 NAC transcription factors that clustered into six major groups were used in the phylogenetic analysis. Many orthologous groups were found in the monocot and eudicot lineages, but only five orthologous groups were found between P. patens and each representative taxa of flowering plants. These groups were called basal orthologous groups and likely expanded into more recent taxa to cope with their environmental needs. This analysis on the angiosperm NAC family represents an effort to grasp the evolutionary and functional diversity within this gene family while providing a basis for further functional research on vascular plant gene families.

Barriers to microbial migrations can lead adaptive radiations and increased endemism. We propose that extreme unbalanced nutrient stoichiometry of essential nutrients can be a barrier to microbial immigration over geological timescales. At the oasis in the Cuatro Ciénegas Basin in Mexico, nutrient stoichiometric proportions are skewed given the low phosphorus availability in the ecosystem. We show that this endangered oasis can be a model for a lost world. The ancient niche of extreme unbalanced nutrient stoichiometry favoured survival of ancestral microorganisms. This extreme nutrient imbalance persisted due to environmental stability and low extinction rates, generating a diverse and unique bacterial community. Several endemic clades of Bacillus invaded the Cuatro Cienegas region in two geological times, the late Precambrian and the Jurassic. Other lineages of Bacillus, Clostridium and Bacteroidetes migrated into the basin in isolated events. Cuatro Ciénegas Basin conservation is vital to the understanding of early evolutionary and ecological processes. Water is a rare sight in a barren land, but there are many more reasons that make the Cuatro Cienegas Basin, an oasis in the North Mexican desert, a puzzling environment. With little phosphorous and nutrients but plenty of sulphur and magnesium, the conditions in the turquoise blue lagoons of the Basin mimic the ones found in the ancient seas of the end of the Precambrian. In fact, Cuatro Cienegas is one of the rare sites where we can still find live stromatolites, a bacterial form of life that once dominated the oceans. Many bacteria of marine origin exist alongside these living fossils, prompting scientists to wonder if the Basin could be a true lost world, a safe haven where ancient microorganisms found refuge and have kept evolving until this day. But to confirm whether this is the case would require scientists to hunt for clues within the genetic information of local bacteria. Souza, Moreno-Letelier et al. came across these hints after sampling for bacteria in a small (about 1km2) lagoon named Churince, and analysing the DNA collected. The results yielded an astonishing amount of biodiversity: 5,167 species representing at least two-third of all known major groups of bacteria were identified, nearly as much as what was found in over 2,000 kilometres in the Pearl River in China. This is unusual, as most other extreme environments with little nutrients have low levels of diversity. Closer investigation into the genomes of 2,500 species of Bacillus bacteria revealed that the sample increased by nearly 21% the number of previously known species in the group. Most of these bacteria were only found in the Basin. These native or ‘endemic’ species have evolved from ancestors that came to the area in two waves. The oldest colonization event happened 680 million years ago, as the first animal forms just started to emerge. The most recent one took place while dinosaurs roamed the Earth about 160 million years ago, when geological events opened again the Basin to the ancient Pacific Ocean. Previous experiments have shown that different species of bacteria in the Churince have evolved to form a close-knit community which ferociously competes with microbes from the outside world. Paired with the extreme conditions found in the lagoon, this may have prevented other microorganisms from proliferating in the environment and replacing the ancient lineages. The days of this lost world may now be numbered. Drained by local farming, the wetlands of the Basin have shrunk by 90% over the past five decades. The Churince lagoon, the most diverse and fragile site where the samples were collected, is now completely dry. Human activities also disrupt the delicate and unique balance of nutrients in the oasis. But all may not be lost – yet. Local high school students have become involved in the research effort to describe and protect these unique microbial communities, and to change agricultural traditions in the area. Closing the canals that export spring water out of the Basin could give the site a chance to recover, and the microbes that are now seeking refuge in underground waters could re-emerge. Maybe there will still be time to celebrate, rather than mourn, the unique life forms of the Cuatro Cienegas Basin.

The genome and transcriptome sequences of the aquatic, rootless, and carnivorous plant Utricularia gibba L. (Lentibulariaceae), were recently determined. Traps are necessary for U. gibba because they help the plant to survive in nutrient-deprived environments. The U. gibba's traps (Ugt) are specialized structures that have been proposed to selectively filter microbial inhabitants. To determine whether the traps indeed have a microbiome that differs, in composition or abundance, from the microbiome in the surrounding environment, we used whole-genome shotgun (WGS) metagenomics to describe both the taxonomic and functional diversity of the Ugt microbiome. We collected U. gibba plants from their natural habitat and directly sequenced the metagenome of the Ugt microbiome and its surrounding water. The total predicted number of species in the Ugt was more than 1,100. Using pan-genome fragment recruitment analysis, we were able to identify to the species level of some key Ugt players, such as Pseudomonas monteilii. Functional analysis of the Ugt metagenome suggests that the trap microbiome plays an important role in nutrient scavenging and assimilation while complementing the hydrolytic functions of the plant.

Understanding the principles that govern community assemblages is a central goal of ecology. There is limited experimental evidence in natural settings showing that microbial assembly in communities are influenced by antagonistic interactions. We, therefore, analyzed antagonism among bacterial isolates from a taxonomically related bacterial guild obtained from five sites in sediments from a fresh water system. We hypothesized that if antagonistic interactions acted as a shaping force of the community assembly, then the frequency of resistance to antagonism among bacterial isolates originating from a given site would be higher than the resistance to conspecifics originating from a different assemblage. Antagonism assays were conducted between 78 thermoresistant isolates, of which 72 were Bacillus spp. Sensitive, resistant and antagonistic isolates co-occurred at each site, but the within-site frequency of resistance observed was higher than that observed when assessed across-sites. We found that antagonism results from bacteriocin-like substances aimed at the exclusion of conspecifics. More than 6000 interactions were scored and described by a directed network with hierarchical structure that exhibited properties that resembled a food chain, where the different Bacillus taxonomic groups occupied specific positions. For some tested interacting pairs, the unidirectional interaction could be explained by competition that inhibited growth or completely excluded one of the pair members. This is the first report on the prevalence and specificity of Bacillus interactions in a natural setting and provides evidence for the influence of bacterial antagonist interactions in the assemblage of a taxonomically related guild in local communities.

Cockatiels ( ) were originally endemic to Australia; now they are popular pets with a global distribution. It is now possible to conduct detailed molecular studies on cultivable and uncultivable bacteria that are part of the intestinal microbiome of healthy animals. These studies show that bacteria are an essential part of the metabolic capacity of animals. There are few studies on bird microbiomes and, to the best of our knowledge, this is the first report on the cockatiel microbiome. In this paper, we analyzed the gut microbiome from fecal samples of three healthy adult cockatiels by massive sequencing of the 16S rRNA gene. Additionally, we compared the cockatiel fecal microbiomes with those of other bird species, including poultry and wild birds. The vast majority of the bacteria found in cockatiels were , while and were poorly represented. A total of 19,280 different OTUs were detected, of which 8,072 belonged to the family. It is relevant to study cockatiel the microbiomes of cockatiels owing to their wide geographic distribution and close human contact. This study serves as a reference for cockatiel bacterial diversity. Despite the large OTU numbers, the diversity is not even and is dominated by of the family. Cockatiels and other wild birds are almost depleted of , which happen to be abundant in poultry-related birds, and this is probably associated with the intensive human manipulation of poultry bird diets. Some probable pathogenic bacteria, such as and appeared to be frequent inhabitants of the fecal microbiome of cockatiels, whereas other potential pathogens were not detected.

The ethylene-responsive element-binding factors AP2/ERF compose one of the largest families of transcription factors in plants. Dreb2-type gene from Carica papaya L. cv. Maradol was found to be a member of the AP2/ERF family and contains a conserved APETALA 2 (AP2) domain located within the group IV of the AP2/ERF superfamily. CpDreb2-type gene is differentially expressed under stress by extreme temperatures. Moreover, genetic transformation of tobacco plants that overexpress the CpDreb2-type gene showed an increase amount of proline and a greater tolerance level to low and high temperature as well as drought experiments. CpDREB2-type protein::GFP is localized mainly in the nuclei of cells from specific organs such as roots and leaves in tobacco seedlings. Our results indicate that CpDreb2-type gene can be used to gain tolerance to extreme conditions of temperature and drought in other plants.

The metro is one of the more representative urban transportation systems of Mexico City, and it transports approximately 4.5 million commuters every day. Large crowds promote the exchange of microbes between humans. In this study, we determined the bacterial diversity profile of the Mexico City metro by massive sequencing of the 16S rRNA gene. We identified a total of 50,174 operational taxonomic units (OTUs) and 1058 genera. The metro microbiome was dominated by the phylum Actinobacteria and by the genera Cutibacterium (15%) ( C. acnes 13%), Corynebacterium (13%), Streptococcus (9%), and Staphylococcus (5%) ( S. epidermidis; 4%), reflecting the microbe composition of healthy human skin. The metro likely microbial sources were skin, dust, saliva, and vaginal, with no fecal contribution detected. A total of 420 bacterial genera were universal to the twelve metro lines tested, and those genera contributed to 99.10% of the abundance. The annual 1.6 billion ridership makes this public transport a main hub for microbe-host-environment interactions. Finally, this study shows that the microbial composition of the Mexico City metro comes from a mixture of environmental and human sources and that commuters are exposed to healthy composition of the human microbiota.

Irritable bowel syndrome (IBS) is the most frequent functional gastrointestinal disorder, worldwide, with a high prevalence among Mestizo Latin Americans. Because several inflammatory disorders appear to affect this population, a further understanding of host genomic background variants, in conjunction with colonic mucosa dysbiosis, is necessary to determine IBS physiopathology and the effects of environmental pressures. Using a simple polygenic model, host single nucleotide polymorphisms (SNPs) and the taxonomic compositions of microbiota were compared between IBS patients and healthy subjects. As proof of concept, five IBS-Rome III patients and five healthy controls (HCs) were systematically studied. The human and bacterial intestinal metagenome of each subject was taxonomically annotated and screened for previously annotated IBS, ulcerative colitis, and Crohn's disease-associated SNPs or taxon abundance. Dietary data and fecal markers were collected and associated with the intestinal microbiome. However, more than 1,000 variants were found, and at least 76 SNPs differentiated IBS patients from HCs, as did associations with 4 phyla and 10 bacterial genera. In this study, we found elements supporting a polygenic background, with frequent variants, among the Mestizo population, and the colonic mucosal enrichment of , and , may serve as a hallmark for IBS.

The oral cavity of humans is inhabited by hundreds of bacterial species and some of them have a key role in the development of oral diseases, mainly dental caries and periodontitis. We describe for the first time the metagenome of the human oral cavity under health and diseased conditions, with a focus on supragingival dental plaque and cavities. Direct pyrosequencing of eight samples with different oral-health status produced 1 Gbp of sequence without the biases imposed by PCR or cloning. These data show that cavities are not dominated by Streptococcus mutans (the species originally identified as the ethiological agent of dental caries) but are in fact a complex community formed by tens of bacterial species, in agreement with the view that caries is a polymicrobial disease. The analysis of the reads indicated that the oral cavity is functionally a different environment from the gut, with many functional categories enriched in one of the two environments and depleted in the other. Individuals who had never suffered from dental caries showed an over-representation of several functional categories, like genes for antimicrobial peptides and quorum sensing. In addition, they did not have mutans streptococci but displayed high recruitment of other species. Several isolates belonging to these dominant bacteria in healthy individuals were cultured and shown to inhibit the growth of cariogenic bacteria, suggesting the use of these commensal bacterial strains as probiotics to promote oral health and prevent dental caries.

Phytostabilization is a remediation technology that uses plants for in-situ stabilization of contamination in soils and mine tailings. The objective of this study was to identify native plant species with potential for phytostabilization of the abandoned mine tailings in Nacozari, Sonora in northern Mexico. A flora of 42 species in 16 families of angiosperms was recorded on the tailings site and the abundance of the most common perennial species was estimated. Four of the five abundant perennial species showed evidence of regeneration: the ability to reproduce and establish new seedlings. A comparison of selected physicochemical properties of the tailings in vegetated patches with adjacent barren areas suggests that pH, electrical conductivity, texture, and concentration of potentially toxic elements do not limit plant distribution. For the most abundant species, the accumulation factor for most metals was <1, with the exception of Zn in two species. A short-term experiment on adaptation revealed limited evidence for the formation of local ecotypes in Prosopis velutina and Amaranthus watsonii . Overall, the results of this study indicate that five native plant species might have potential for phytostabilization of the Nacozari tailings and that seed could be collected locally to revegetate the site. More broadly, this study provides a methodology that can be used to identify native plants and evaluate their phytostabilization potential for similar mine tailings.