Alejandro López-Cortés

Bio: Alejandro López-Cortés is an academic researcher from Spanish National Research Council. The author has contributed to research in topics: Microbial ecology & Microbial mat. The author has an hindex of 17, co-authored 39 publications receiving 1587 citations. Previous affiliations of Alejandro López-Cortés include Max Planck Society.

Phosphate-solubilizing microorganisms associated with the rhizosphere of mangroves in a semiarid coastal lagoon

Abstract: The phosphate-solubilizing potential of the rhizosphere microbial community in mangroves was de- monstrated when culture media supplemented with in- soluble, tribasic calcium phosphate, and incubated with roots of black (Avicennia germinans L.) and white (La- guncularia racemosa (L.) Gaertn.) mangrove became transparent after a few days of incubation. Thirteen phosphate-solubilizing bacterial strains were isolated from the rhizosphere of both species of mangroves: Ba- cillus amyloliquefaciens, Bacillus licheniformis, Bacillus atrophaeus, Paenibacillus macerans, Vibrio proteolyti- cus, Xanthobacter agilis, Enterobacter aerogenes, Ente- robacter taylorae, Enterobacter asburiae, Kluyvera cryo- crescens, Pseudomonas stutzeri, and Chryseomonas lu- teola. One bacterial isolate could not be identified. The rhizosphere of black mangroves also yielded the fungus Aspergillus niger. The phosphate-solubilizing activity of the isolates was first qualitatively evaluated by the for- mation of halos (clear zones) around the colonies grow- ing on solid medium containing tribasic calcium phos- phate as a sole phosphorus source. Spectrophotometric quantification of phosphate solubilization showed that all bacterial species and A. niger solubilized insoluble phosphate well in a liquid medium, and that V. proteo- lyticus was the most active solubilizing species among the bacteria. Gas chromatographic analyses of cell-free spent culture medium from the various bacteria de- monstrated the presence of 11 identified, and several unidentified, volatile and nonvolatile organic acids. Those most commonly produced by different species were lactic, succinic, isovaleric, isobutyric, and acetic acids. Most of the bacterial species produced more than one organic acid whereas A. niger produced only suc- cinic acid. We propose the production of organic acids by these mangrove rhizosphere microorganisms as a possible mechanism involved in the solubilization of in- soluble calcium phosphate.

Phylogenetic and Morphological Diversity of Cyanobacteria in Soil Desert Crusts from the Colorado Plateau

Abstract: We compared the community structures of cyanobacteria in four biological desert crusts from Utah's Colorado Plateau developing on different substrata. We analyzed natural samples, cultures, and cyanobacterial filaments or colonies retrieved by micromanipulation from field samples using microscopy, denaturing gradient gel electrophoresis, and sequencing of 16S rRNA genes. While microscopic analyses apparently underestimated the biodiversity of thin filamentous cyanobacteria, molecular analyses failed to retrieve signals for otherwise conspicuous heterocystous cyanobacteria with thick sheaths. The diversity found in desert crusts was underrepresented in currently available nucleotide sequence databases, and several novel phylogenetic clusters could be identified. Morphotypes fitting the description of Microcoleus vaginatus Gomont, dominant in most samples, corresponded to a tight phylogenetic cluster of probable cosmopolitan distribution, which was well differentiated from other cyanobacteria traditionally classified within the same genus. A new, diverse phylogenetic cluster, named "Xeronema," grouped a series of thin filamentous Phormidium-like cyanobacteria. These were also ubiquitous in our samples and probably correspond to various botanical Phormidium and Schizothrix spp., but they are phylogenetically distant from thin filamentous cyanobacteria from other environments. Significant differences in community structure were found among soil types, indicating that soil characteristics may select for specific cyanobacteria. Gypsum crusts were most deviant from the rest, while sandy, silt, and shale crusts were relatively more similar among themselves.

Screening and Isolation of PHB-Producing Bacteria in a Polluted Marine Microbial Mat

Abstract: The characteristics of microbial mats within the waste stream from a seafood cannery were compared to a microbial community at a pristine site near a sandy beach at Puerto San Carlos, Baja California Sur, Mexico. Isolation of poly-β-hydroxybutyrate (PHB)-producing bacteria, recognition of brightly refractile cytoplasmatic inclusions, lipophilic stains with Sudan Black and Nile Red, and chemical extraction of PHB were used as a culture-dependent strategy for the detection of PHB-producing bacteria. The culture-independent approach included denaturing gradient gel electrophoresis of phylotypes of 16S rRNA of microbial communities from environmental samples. Significant differences in community structure were found among the polluted and pristine sites. These differences were correlated with the physicochemical characteristics of the seawater column. At the polluted site, the seawater was rich in nutrients (ammonia, phosphates, and organic matter), compared to the pristine location. Partial sequencing of 16S rDNA of cultures of bacteria producing PHB included Bacillus and Staphylococcus at both sites; Paracoccus and Micrococcus were found only at the polluted site and Rhodococcus and Methylobacterium were found only at the pristine site. Bands of the sequences of 16S rDNA from both field samples in the denaturing gradient gel electrophoresis (DGGE) analyses affiliated closely only with bacterial sequences of cultures of Bacillus and Staphylococcus. High concentrations of organic and inorganic nutrients at the polluted site had a clear effect on the composition and diversity of the microbial community compared to the unpolluted site.

Plant growth promoting rhizobacteria as biofertilizers

Abstract: Numerous species of soil bacteria which flourish in the rhizosphere of plants, but which may grow in, on, or around plant tissues, stimulate plant growth by a plethora of mechanisms. These bacteria are collectively known as PGPR (plant growth promoting rhizobacteria). The search for PGPR and investigation of their modes of action are increasing at a rapid pace as efforts are made to exploit them commercially as biofertilizers. After an initial clarification of the term biofertilizers and the nature of associations between PGPR and plants (i.e., endophytic versus rhizospheric), this review focuses on the known, the putative, and the speculative modes-of-action of PGPR. These modes of action include fixing N2, increasing the availability of nutrients in the rhizosphere, positively influencing root growth and morphology, and promoting other beneficial plant–microbe symbioses. The combination of these modes of actions in PGPR is also addressed, as well as the challenges facing the more widespread utilization of PGPR as biofertilizers.

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Abstract: Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

The ecology and biotechnology of sulphate-reducing bacteria

Abstract: Sulphate-reducing bacteria (SRB) are anaerobic microorganisms that use sulphate as a terminal electron acceptor in, for example, the degradation of organic compounds. They are ubiquitous in anoxic habitats, where they have an important role in both the sulphur and carbon cycles. SRB can cause a serious problem for industries, such as the offshore oil industry, because of the production of sulphide, which is highly reactive, corrosive and toxic. However, these organisms can also be beneficial by removing sulphate and heavy metals from waste streams. Although SRB have been studied for more than a century, it is only with the recent emergence of new molecular biological and genomic techniques that we have begun to obtain detailed information on their way of life.

Biology of mangroves and mangrove Ecosystems

Abstract: Mangroves are woody plants that grow at the interface between land and sea in tropical and sub-tropical latitudes where they exist in conditions of high salinity, extreme tides, strong winds, high temperatures and muddy, anaerobic soils. There may be no other group of plants with such highly developed morphological and physiological adaptations to extreme conditions. Because of their environment, mangroves are necessarily tolerant of high salt levels and have mechanisms to take up water despite strong osmotic potentials. Some also take up salts, but excrete them through specialized glands in the leaves. Others transfer salts into senescent leaves or store them in the bark or the wood. Still others simply become increasingly conservative in their water use as water salinity increases Morphological specializations include profuse lateral roots that anchor the trees in the loose sediments, exposed aerial roots for gas exchange and viviparous waterdispersed propagules. Mangroves create unique ecological environments that host rich assemblages of species. The muddy or sandy sediments of the mangal are home to a variety of epibenthic, infaunal, and meiofaunal invertebrates Channels within the mangal support communities of phytoplankton, zooplankton and fish. The mangal may play a special role as nursery habitat for juveniles of fish whose adults occupy other habitats (e.g. coral reefs and seagrass beds). Because they are surrounded by loose sediments, the submerged mangroves' roots, trunks and branches are islands of habitat that may attract rich epifaunal communities including bacteria, fungi, macroalgae and invertebrates. The aerial roots, trunks, leaves and branches host other groups of organisms. A number of crab species live among the roots, on the trunks or even forage in the canopy. Insects, reptiles, amphibians, birds and mammals thrive in the habitat and contribute to its unique character. Living at the interface between land and sea, mangroves are well adapted to deal with natural stressors (e.g. temperature, salinity, anoxia, UV). However, because they live close to their tolerance limits, they may be particularly sensitive to disturbances like those created by human activities. Because of their proximity to population centers, mangals have historically been favored sites for sewage disposal. Industrial effluents have contributed to heavy metal contamination in the sediments. Oil from spills and from petroleum production has flowed into many mangals. These insults have had significant negative effects on the mangroves. Habitat destruction through human encroachment has been the primary cause of mangrove loss. Diversion of freshwater for irrigation and land reclamation has destroyed extensive mangrove forests. In the past several decades, numerous tracts of mangrove have been converted for aquaculture, fundamentally altering the nature of the habitat. Measurements reveal alarming levels of mangrove destruction. Some estimates put global loss rates at one million ha y−1, with mangroves in some regions in danger of complete collapse. Heavy historical exploitation of mangroves has left many remaining habitats severely damaged. These impacts are likely to continue, and worsen, as human populations expand further into the mangals. In regions where mangrove removal has produced significant environmental problems, efforts are underway to launch mangrove agroforestry and agriculture projects. Mangrove systems require intensive care to save threatened areas. So far, conservation and management efforts lag behind the destruction; there is still much to learn about proper management and sustainable harvesting of mangrove forests. Mangroves have enormous ecological value. They protect and stabilize coastlines, enrich coastal waters, yield commercial forest products and support coastal fisheries. Mangrove forests are among the world's most productive ecosystems, producing organic carbon well in excess of the ecosystem requirements and contributing significantly to the global carbon cycle. Extracts from mangroves and mangrove-dependent species have proven activity against human, animal and plant pathogens. Mangroves may be further developed as sources of high-value commercial products and fishery resources and as sites for a burgeoning ecotourism industry. Their unique features also make them ideal sites for experimental studies of biodiversity and ecosystem function. Where degraded areas are being revegetated, continued monitoring and thorough assessment must be done to help understand the recovery process. This knowledge will help develop strategies to promote better rehabilitation of degraded mangrove habitats the world over and ensure that these unique ecosystems survive and flourish.

Phosphate solubilizing microbes: sustainable approach for managing phosphorus deficiency in agricultural soils

Abstract: Phosphorus is the second important key element after nitrogen as a mineral nutrient in terms of quantitative plant requirement. Although abundant in soils, in both organic and inorganic forms, its availability is restricted as it occurs mostly in insoluble forms. The P content in average soil is about 0.05% (w/w) but only 0.1% of the total P is available to plant because of poor solubility and its fixation in soil (Illmer and Schinner, Soil Biol Biochem 27:257-263, 1995). An adequate supply of phosphorus during early phases of plant development is important for laying down the primordia of plant reproductive parts. It plays significant role in increasing root ramification and strength thereby imparting vitality and disease resistance capacity to plant. It also helps in seed formation and in early maturation of crops like cereals and legumes. Poor availability or deficiency of phosphorus (P) markedly reduces plant size and growth. Phosphorus accounts about 0.2 - 0.8% of the plant dry weight. To satisfy crop nutritional requirements, P is usually added to soil as chemical P fertilizer, however synthesis of chemical P fertilizer is highly energy intensive processes, and has long term impacts on the environment in terms of eutrophication, soil fertilility depletion, carbon footprint. Moreover, plants can use only a small amount of this P since 75–90% of added P is precipitated by metal–cation complexes, and rapidly becomes fixed in soils. Such environmental concerns have led to the search for sustainable way of P nutrition of crops. In this regards phosphate-solubilizing microorganisms (PSM) have been seen as best eco-friendly means for P nutrition of crop. Although, several bacterial (pseudomonads and bacilli) and fungal strains (Aspergilli and Penicillium) have been identified as PSM their performance under in situ conditions is not reliable and therefore needs to be improved by using either genetically modified strains or co-inoculation techniques. This review focuses on the diversity of PSM, mechanism of P solubilization, role of various phosphatases, impact of various factors on P solubilization, the present and future scenario of their use and potential for application of this knowledge in managing a sustainable environmental system.