Metagenomics is a culture-independent technology that allows access to novel and potentially useful genetic resources from a wide range of unknown microorganisms. In this study, a fosmid metagenomic ...library of tropical underground water was constructed, and clones were functionally screened for extracellular proteolytic activity. One of the positive clones, containing a 41,614-bp insert, had two genes with 60% and 68% identity respectively with a peptidase S8 of Chitinimonas koreensis. When these genes were individually sub-cloned, in both cases their sub-clones showed proteolytic phenotype, confirming that they both encode functional proteases. These genes –named PrAY5 and PrAY6- are next to each other. They are similar in size (1845bp and 1824bp respectively) and share 66.5% identity. An extensive in silico characterization showed that their ORFs encode complex zymogens having a signal peptide at their 5′ end, followed by a pro-peptide, a catalytic region, and a PPC domain at their 3′ end. Their translated sequences were classified as peptidases S8A by sequence comparisons against the non-redundant database and corroborated by Pfam and MEROPS. Phylogenetic analysis of the catalytic region showed that they encode novel proteases that clustered with the sub-family S8_13, which according to the CDD database at NCBI, is an uncharacterized subfamily. They clustered in a clade different from the other three proteases S8 found so far by functional metagenomics, and also different from proteases S8 found in sequenced environmental samples, thereby expanding the range of potentially useful proteases that have been identified by metagenomics. I-TASSER modeling corroborated that they may be subtilases, thus possibly they participate in the hydrolysis of proteins with broad specificity for peptide bonds, and have a preference for a large uncharged residue in P1.
•A fosmid metagenomic library of tropical underground water was constructed.•Two novel protease S8A genes were identified by functional screening.•An extensive in silico characterization showed that their ORFs encode complex zymogens.•Independent sub-cloning of these two genes showed that both encode functional proteases.•Modeling suggests that they encode subtilases which hydrolyze a broad range of peptide bonds.
In Neotropical regions, plantations and remnant forest populations of native trees coexist in a highly fragmented matrix and may be affected by isolation and reduction in population size, leading to ...genetic structure, inbreeding, and genetic bottlenecks that reduce the population’s genetic diversity. Tabebuia rosea variability in the Mayan Forest was studied by genotyping 30 trees from three plantations and three remnant natural populations using simple sequence repeats (SSRs) and inter-simple sequence repeats (ISSRs). Ho-SSR estimates were lower than He; the mean inbreeding coefficient was 0.07 and did not differ among populations, but was eight times higher in plantations than in remnant populations. Using ISSR data, the individuals were assigned to k = 5 and k = 4 clusters under admixture without and with geographic information used as priors in Bayesian analysis assignments. Genetic differentiation estimated with the Bayesian estimator II (0.0275 ± 0.0052) was significantly different from 0, but FST was not (0.0985 ± 0.1826), while paired FST among populations ranged from 0.05 up to 0.16. Only one remnant population displayed evidence of a genetic bottleneck. T. rosea displays a genetic structure in which the isolated remnant forest populations show moderate inbreeding levels.
Swietenia macrophylla is a tropical timber species of ecological and economic importance. However, its slow vegetative growth and root development in nurseries strongly limit its production. This ...study evaluated the effect of 10 rhizobacteria strains during the early stages of production of S. macrophylla. Superficially disinfected seeds were inoculated with rhizobacteria under commercial nursery conditions. Inoculation was complemented by initial fertilization without growth regulators, fungicides, or bactericides. The results indicate that the rhizobacteria strains induce different responses in plants. Significant differences in plant biomass and root architecture were found. Treatments inoculated with Bacillus sp., Bacillus polyfermenticus, and Bacillus siamensis strains; showed an increase of up to 41% (dry weight). Plants increased root biomass by 30% when inoculated with S. siamensis. All inoculated strains were identified as members of the genus Bacillus spp., and their presence three months after inoculation was assessed by 16S rRNA gene-based amplicon massive sequencing. We found that Bacillus sp. genus was only present in inoculated treatments, suggesting that inoculated bacteria could establish themselves successfully as part of the microbiota. These results support the advantages of using PGPRs in commercial tropical tree production.
During domestication, the selection of cultivated plants often reduces microbiota diversity compared with their wild ancestors. Microbiota in compartments such as the phyllosphere or rhizosphere can ...promote fruit tree health, growth, and development.
is a deciduous tree used by Maya people for its fruit and wood, growing, to date, in remnant forest fragments and homegardens (traditional agroforestry systems) in Yucatán. In this work, we evaluated the microbiota's alpha and beta diversity per compartment (phyllosphere and rhizosphere) and per population (forest and homegarden) in the Northeast and Southwest Yucatán regions. Eight composite DNA samples (per compartment/population/region combination) were amplified for 16S-RNA (bacteria) and ITS1-2 (fungi) and sequenced by Illumina MiSeq. Bioinformatic analyses were performed with QIIME and phyloseq. For bacteria and fungi, from 107,947 and 128,786 assembled sequences, 618 and 1092 operating taxonomic units (OTUs) were assigned, respectively. The alpha diversity of bacteria and fungi was highly variable among samples and was similar among compartments and populations. A significant species turnover among populations and regions was observed in the rhizosphere. The core microbiota from the phyllosphere was similar among populations and regions. Forests and homegarden populations are reservoirs of the
phyllosphere core microbiome and significant rhizosphere biodiversity.
Bacterial communities have been identified as functional key members in soil ecology. A deep relation with these communities maintains forest coverture. Trees harbor particular bacteriomes in the ...rhizosphere, endosphere, or phyllosphere, different from bulk-soil representatives. Moreover, the plant microbiome appears to be specific for the plant-hosting species, varies through season, and responsive to several environmental factors. This work reports the changes in bacterial communities associated with dominant pioneer trees
Tabebuia rosea
and
Handroanthus chrysanthus
(Bignoniaceae) during tropical forest recovery chronosequence in the Mayan forest in Campeche, Mexico. Massive 16S sequencing approach leads to identifying phylotypes associated with rhizosphere, bulk-soil, or recovery stage. Lotka–Volterra interactome modeling suggests the presence of putative regulatory roles of some phylotypes over the rest of the community. Our results may indicate that bacterial communities associated with pioneer trees may establish more complex regulatory networks than those found in bulk-soil. Moreover, modeled regulatory networks predicted from rhizosphere samples resulted in a higher number of nodes and interactions than those found in the analysis of bulk-soil samples.
Spanish red cedar,
Cedrela odorata
L. (Meliaceae), is a valuable timber tree in tropical American forests. Existing demand for elite individuals endangers the conservation of interesting germplasm, ...prompting the development of efficient protocols for the establishment of orchards for tree breeding. Based on previous work regarding grafting adult individuals onto young rootstocks, superior trees from Calakmul Biosphere Reserve in Campeche, Mexico were employed as a source of explants for plant regeneration after successive rounds of grafting and micrografting onto juvenile rootstocks. The results showed that root length and appearance, internode distance, leaf length and number, and plant height values for trees derived from successive rounds of grafting and micrografting were similar to those obtained from juvenile trees derived from seeds, suggesting that developmental traits associated with reinvigoration were partially induced following the reported procedure. This protocol may be useful for the propagation of mature elite trees belonging to the Meliaceae family.
Marine invertebrate-associated microbial communities are interesting examples of complex symbiotic systems and are a potential source of biotechnological products.
In this work, pyrosequencing-based ...assessment from bacterial community structures of sediments, two sponges, and one zoanthid collected in the Mexican Caribbean was performed. The results suggest that the bacterial diversity at the species level is higher in the sediments than in the animal samples. Analysis of bacterial communities' structure showed that about two thirds of the bacterial diversity in all the samples belongs to the phyla Acidobacteria and Proteobacteria. The genus Acidobacterium appears to dominate the bacterial community in all the samples, reaching almost 80% in the sponge Hyrtios.
Our evidence suggests that the sympatric location of these benthonic species may lead to common bacterial structure features among their bacterial communities. The results may serve as a first insight to formulate hypotheses that lead to more extensive studies of sessile marine organisms' microbiomes from the Mexican Caribbean.
Agave tequilana Weber var. 'Azul' is grown for the production of tequila, inulin and syrup. Diverse bacteria inhabit plant tissues and play a crucial role for plant health and growth. In this study ...culturable endophytic bacteria were extracted from leaf bases of 100 healthy Agave tequilana plants. In plant tissue bacteria occurred at mean population densities of 3 million CFU/g of fresh plant tissue. Three hundred endophytic strains were isolated and 16s rDNA sequences grouped the bacteria into eight different taxa that shared high homology with other known sequences. Bacterial endophytes were identified as Acinectobacter sp., A. baumanii, A. bereziniae, Cronobacter sakazakii, Enterobacter hormaechei, Bacillus sp. Klebsiella oxytoca, Pseudomonas sp., Enterococcus casseliflavus, Leuconostoc mesenteroides subsp. mesenteroides and Gluconobacter oxydans. Isolates were confirmed to be plant growth promoting bacteria (PGPB) by their capacities for nitrogen fixation, auxin production, phosphate solubilization, or antagonism against Fusarium oxysporum AC132. E. casseliflavus JM47 and K. oxytoca JM26 secreted the highest concentrations of IAA. The endophyte Acinectobacter sp. JM58 exhibited the maximum values for nitrogen fixation and phosphate solubilization index (PSI). Inhibition of fungi was found in Pseudomonas sp. JM9p and K. oxytoca JM26. Bacterial endophytes show promise for use as bio-inoculants for agave cultivation. Use of endophytes to enhance cultivation of agave may be particularly important for plants produced by micropropagation techniques, where native endophytes may have been lost.
Tree planters of the Yucatan peninsula in México are mostly first-generation small-scale forest owners. As a consequence of the lack of a management plan, trees employed for plantations are currently ...produced without any traceability or genetic improvement protocol, resulting in the reduced quality and heterogeneity of established materials. Recently, the Mexican government published a law to force planters to reverse this situation through the initiation and operation of germplasm management and traceability programs within each physiographic sub-province. Thus, planters located in the “Campeche Karts sub-provenance” now need to select superior trees for plant production, provenance assays, and orchard establishment. As a reference for the improvement goals in this work, we developed a model ideotype tree and qualification tool based on a weight-free selection index to compare trees in established plantations to enable the effective selection of superior trees to be used as seed sources and as a starting population for genetic improvement programs. The tool presented here is easy to use by planters, requiring a very basic computer or smartphone to run a spreadsheet where simple morphometric evaluation are captured, trees are qualified in comparison to the ideotypic values of each parameter with the aid of common field equipment. When this tool was applied to individuals from two different plantations, the qualification methodology ranked the individuals, allowing for the selection of superior trees in a more robust way, in contrast to the use of parameters mostly based on price and driven by wood volume.
Spanish red cedar (
Cedrela
odorata
L.) is a tropical timber tree native to the Americas from southern Mexico to northern Argentina. Commercial plantations are scarce and, consequently, natural ...populations are overexploited. Traditional propagation practices for the establishment of large-scale plantations have had limited success in this species due to the relative scarcity of seeds, its broad genetic diversity and the lack of domesticated varieties. In vitro clonal propagation provides an effective method to overcome this situation and increase the yield of commercial plantations through the rapid multiplication of elite materials. Somatic embryogenesis (SE) is one of the most promising strategies for tree propagation due to the possibility of producing artificial seeds, the ability to store and rapidly mobilize germplasm and the opportunity for genetic manipulation. We report here the induction of indirect SE in
C. odorata
from calli derived from immature zygotic embryos after 12 weeks of culture. Macroscopic, histological, and scanning electron microscopic analyses of the calli revealed the presence of embryogenic cell clusters that formed cotyledonary embryos with clear bipolar structures and no vascular connections with the mother tissue. Different media preparations containing combinations of diverse auxins and cytokinins are known to have different effects on the type and frequency of embryogenic structures. Embryo conversion was achieved using an MS-based medium Murashige T, Skoog F (1962) Physiol Plant 15:473–497, 1962 supplemented with abscisic acid, and transfer to soil was successful at a rate of 75%. The method described here provides a basis for optimizing the clonal propagation and genetic manipulation of this valuable species.
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