Genetic analysis of Vibrio parahaemolyticus O3:K6 strains that have been isolated in Mexico since 1998

CARLOS ABRAHAM GUERRERO RUIZ (2017, [Artículo])

Vibrio parahaemolyticus is an important human pathogen that has been isolated worldwide from clinical cases, most of which have been associated with seafood consumption. Environmental and clinical toxigenic strains of V. parahaemolyticus that were isolated in Mexico from 1998 to 2012, including those from the only outbreak that has been reported in this country, were characterized genetically to assess the presence of the O3:K6 pandemic clone, and their genetic relationship to strains that are related to the pandemic clonal complex (CC3). Pathogenic tdh+ and tdh+/trh+ strains were analyzed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Also, the entire genome of a Mexican O3:K6 strain was sequenced. Most of the strains were tdh/ORF8-positive and corresponded to the O3:K6 serotype. By PFGE and MLST, there was very close genetic relationship between ORF8/O3:K6 strains, and very high genetic diversities from non-pandemic strains. The genetic relationship is very close among O3:K6 strains that were isolated in Mexico and sequences that were available for strains in the CC3, based on the PubMLST database. The whole-genome sequence of CICESE-170 strain had high similarity with that of the reference RIMD 2210633 strain, and harbored 7 pathogenicity islands, including the 4 that denote O3:K6 pandemic strains. These results indicate that pandemic strains that have been isolated in Mexico show very close genetic relationship among them and with those isolated worldwide. © 2017 Guerrero et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Article, bacterial strain, biofouling, controlled study, Crassostrea, food intake, gene sequence, genetic analysis, genetic variability, Japan, Mexican, Mexico, molecular phylogeny, nonhuman, pandemic, pathogenicity island, sea food, serotyping, toxi BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA GENÉTICA GENÉTICA

Rapid effects of marine reserves via larval dispersal

Richard Cudney Bueno (2009, [Artículo])

Marine reserves have been advocated worldwide as conservation and fishery management tools. It is argued that they can protect ecosystems and also benefit fisheries via density-dependent spillover of adults and enhanced larval dispersal into fishing areas. However, while evidence has shown that marine reserves can meet conservation targets, their effects on fisheries are less understood. In particular, the basic question of if and over what temporal and spatial scales reserves can benefit fished populations via larval dispersal remains unanswered. We tested predictions of a larval transport model for a marine reserve network in the Gulf of California, Mexico, via field oceanography and repeated density counts of recently settled juvenile commercial mollusks before and after reserve establishment. We show that local retention of larvae within a reserve network can take place with enhanced, but spatially-explicit, recruitment to local fisheries. Enhancement occurred rapidly (2 yrs), with up to a three-fold increase in density of juveniles found in fished areas at the downstream edge of the reserve network, but other fishing areas within the network were unaffected. These findings were consistent with our model predictions. Our findings underscore the potential benefits of protecting larval sources and show that enhancement in recruitment can be manifested rapidly. However, benefits can be markedly variable within a local seascape. Hence, effects of marine reserve networks, positive or negative, may be overlooked when only focusing on overall responses and not considering finer spatially-explicit responses within a reserve network and its adjacent fishing grounds. Our results therefore call for future research on marine reserves that addresses this variability in order to help frame appropriate scenarios for the spatial management scales of interest. © 2009 Cudney-Bueno et al.

article, environmental monitoring, fishery, larva, marine environment, marine species, Mexico, mollusc, nonhuman, oceanography, prediction, animal, biology, environmental protection, food industry, geography, growth, development and aging, larva, met CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA CIENCIAS DE LA TIERRA Y DEL ESPACIO OCEANOGRAFÍA OCEANOGRAFÍA

Biodiversity conservation in an anthropized landscape: Trees, not patch size drive, bird community composition in a low-input agroecosystem

ERIC MELLINK BIJTEL (2017, [Artículo])

One of the most typical agro-ecosystems in the Llanos de Ojuelos, a semi-arid region of central Mexico, is that of fruit-production orchards of nopales (prickly pear cacti). This perennial habitat with complex vertical structure provides refuge and food for at least 112 species of birds throughout the year. Nopal orchards vary in their internal structure, size and shrub/ tree composition, yet these factors have unknown effects on the animals that use them. To further understand the conservation potential of this agro-ecosystem, we evaluated the effects of patch-size and the presence of trees on bird community composition, as well as several habitat variables, through an information-theoretical modelling approach. Community composition was obtained through a year of census transects in 12 orchards. The presence of trees in the orchards was the major driver of bird communities followed by seasonality; bird communities are independent of patch size, except for small orchard patches that benefit black-chin sparrows, which are considered a sensitive species. At least 55 species of six trophic guilds (insectivores, granivores, carnivores, nectivores, omnivores, and frugivores) used the orchards. Orchards provide adequate habitat and food resources for several sensitive species of resident and migratory sparrows. The attributes that make orchards important for birds: trees, shrubs, herb seeds, and open patches can be managed to maintain native biodiversity in highly anthropized regions with an urgent need to find convergence between production and biological conservation. © 2017 Mellink et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

agroecosystem, carnivore, chin, conservation biology, driver, frugivore, granivore, habitat, human, insectivore, landscape, nonhuman, omnivore, orchard, resident, seasonal variation, shrub, sparrow, theoretical model, agriculture, animal, biodiversit CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA

Trophic ecology of Mexican Pacific harbor seal colonies using carbon and nitrogen stable isotopes

MARICELA JUAREZ RODRIGUEZ (2020, [Artículo])

There is limited information that provides a comprehensive understanding of the trophic ecology of Mexican Pacific harbor seal (Phoca vitulina richardii) colonies. While scat analysis has been used to determine the diet of some colonies, the integrative characterization of its feeding habits on broader temporal and spatial scales remains limited. We examined potential feeding grounds, trophic niche width, and overlap, and inferred the degree of dietary specialization using stable carbon and nitrogen isotope ratios (δ13C and δ15N) in this subspecies. We analyzed δ13C and δ15N on fur samples from pups collected at five sites along the western coast of the Baja California Peninsula, Mexico. Fur of natal coat of Pacific harbor seal pups begins to grow during the seventh month in utero until the last stage of gestation. Therefore pup fur is a good proxy for the mother's feeding habits in winter (∼December to March), based on the timing of gestation for the subspecies in this region. Our results indicated that the δ13C and δ15N values differed significantly among sampling sites, with the highest mean δ15N value occurring at the southernmost site, reflecting a well-characterized north to south latitudinal 15N-enrichment in the food web. The tendency identified in δ13C values, in which the northern colonies showed the most enriched values, suggests nearshore and benthic-demersal feeding habits. A low variance in δ13C and δ15N values for each colony (<1‰) and relatively small standard ellipse areas suggest a specialized foraging behavior in adult female Pacific harbor seals in Mexican waters. © 2020 Juárez-Rodríguez et al.

carbon, delta carbon 13, delta nitrogen 15, isotope, nitrogen, unclassified drug, carbon, nitrogen, Article, correlational study, feeding behavior, latitude, Mexico, nonhuman, organism colony, Pinnipedia, population abundance, species richness, troph BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA ANIMAL (ZOOLOGÍA) BIOLOGÍA ANIMAL (ZOOLOGÍA)

Assessing the Response of Nematode Communities to Climate Change-Driven Warming: A Microcosm Experiment

RUTH GINGOLD WERMUTH (2013, [Artículo])

Biodiversity has diminished over the past decades with climate change being among the main responsible factors. One consequence of climate change is the increase in sea surface temperature, which, together with long exposure periods in intertidal areas, may exceed the tolerance level of benthic organisms. Benthic communities may suffer structural changes due to the loss of species or functional groups, putting ecological services at risk. In sandy beaches, free-living marine nematodes usually are the most abundant and diverse group of intertidal meiofauna, playing an important role in the benthic food web. While apparently many functionally similar nematode species co-exist temporally and spatially, experimental results on selected bacterivore species suggest no functional overlap, but rather an idiosyncratic contribution to ecosystem functioning. However, we hypothesize that functional redundancy is more likely to observe when taking into account the entire diversity of natural assemblages. We conducted a microcosm experiment with two natural communities to assess their stress response to elevated temperature. The two communities differed in diversity (high [HD] vs. low [LD]) and environmental origin (harsh vs. moderate conditions). We assessed their stress resistance to the experimental treatment in terms of species and diversity changes, and their function in terms of abundance, biomass, and trophic diversity. According to the Insurance Hypothesis, we hypothesized that the HD community would cope better with the stressful treatment due to species functional overlap, whereas the LD community functioning would benefit from species better adapted to harsh conditions. Our results indicate no evidence of functional redundancy in the studied nematofaunal communities. The species loss was more prominent and size specific in the HD; large predators and omnivores were lost, which may have important consequences for the benthic food web. Yet, we found evidence for alternative diversity-ecosystem functioning relationships, such as the Rivets and the Idiosyncrasy Model. © 2013 Gingold et al.

aquaculture, article, bacterivore, benthos, biodiversity, biomass, climate, community dynamics, controlled study, ecosystem, environmental temperature, microcosm, nematode, nonhuman, population abundance, species diversity, species richness, taxonomy CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA CIENCIAS DE LA TIERRA Y DEL ESPACIO OCEANOGRAFÍA OCEANOGRAFÍA

Climate change and the northern elephant seal (Mirounga angustirostris) population in Baja California, Mexico

M. Concepción García-Aguilar (2018, [Artículo])

The Earth0s climate is warming, especially in the mid- and high latitudes of the Northern Hemisphere. The northern elephant seal (Mirounga angustirostris) breeds and haul-outs on islands and the mainland of Baja California, Mexico, and California, U.S.A. At the beginning of the 21st century, numbers of elephant seals in California are increasing, but the status of Baja California populations is unknown, and some data suggest they may be decreasing. We hypothesize that the elephant seal population of Baja California is experiencing a decline because the animals are not migrating as far south due to warming sea and air temperatures. Here we assessed population trends of the Baja California population, and climate change in the region. The numbers of northern elephant seals in Baja California colonies have been decreasing since the 1990s, and both the surface waters off Baja California and the local air temperatures have warmed during the last three decades. We propose that declining population sizes may be attributable to decreased migration towards the southern portions of the range in response to the observed temperature increases. Further research is needed to confirm our hypothesis; however, if true, it would imply that elephant seal colonies of Baja California and California are not demographically isolated which would pose challenges to environmental and management policies between Mexico and the United States. © 2018 García-Aguilar et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

air temperature, article, Baja California, climate change, human, Mirounga angustirostris, nonhuman, population size, warming, animal, ecosystem, environmental protection, Mexico, Phocidae, population density, population migration, temperature, Anima CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA CIENCIAS DE LA TIERRA Y DEL ESPACIO OCEANOGRAFÍA OCEANOGRAFÍA

Whole-genome comparison between reference sequences and oyster Vibrio vulnificus C-genotype strains

CARLOS ABRAHAM GUERRERO RUIZ (2019, [Artículo])

Whole-genome sequences of Vibrio vulnificus clinical genotype (C-genotype) from the CICESE Culture Collection, isolated from oysters, were compared with reference sequences of CMCP6 and YJ016 V. vulnificus C-genotype strains of clinical origin. The RAST web server estimated the whole genome to be ~4.8 Mb in CICESE strain 316 and ~4.7 Mb in CICESE strain 325. No plasmids were detected in the CICESE strains. Based on a phylogenetic tree that was constructed with the whole-genome results, we observed high similarity between the reference sequences and oyster C-genotype isolates and a sharp contrast with environmental genotype (E-genotype) reference sequences, indicating that the differences between the C- and E-genotypes do not necessarily correspond to their isolation origin. The CICESE strains share 3488 genes (63.2%) with the YJ016 strain and 3500 genes (63.9%) with the CMCP6 strain. A total of 237 pathogenicity associated genes were selected from reference clinical strains, where—92 genes were from CMCP6, 126 genes from YJ016, and 19 from MO6-24/ O; the presence or absence of these genes was recorded for the CICESE strains. Of the 92 genes that were selected for CMCP6, 67 were present in both CICESE strains, as were as 86 of the 126 YJ016 genes and 13 of the 19 MO6-24/O genes. The detection of elements that are related to virulence in CICESE strains—such as the RTX gene cluster, vvhA and vvpE, the type IV pili cluster, the XII genomic island, and the viuB genes, suggests that environmental isolates with the C-genotype, have significant potential for infection. © 2019 Guerrero et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Article, bacterial gene, bacterial strain, bacterial virulence, comparative study, controlled study, gene cluster, gene identification, genomic island, genotype, nonhuman, phylogenetic tree, sequence analysis, strain identification, Vibrio vulnificus BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA GENÉTICA GENÉTICA

Gamma-diversity partitioning of gobiid fishes (Teleostei: Gobiidae) ensemble along of Eastern Tropical Pacific: Biological inventory, latitudinal variation and species turnover

OMAR VALENCIA MENDEZ (2018, [Artículo])

Gobies are the most diverse marine fish family. Here, we analysed the gamma-diversity (γ-diversity) partitioning of gobiid fishes to evaluate the additive and multiplicative components of α and β-diversity, species replacement and species loss and gain, at four spatial scales: sample units, ecoregions, provinces and realms. The richness of gobies from the realm Eastern Tropical Pacific (ETP) is represented by 87 species. Along latitudinal and longitudinal gradients, we found that the γ-diversity is explained by the β-diversity at both spatial scales, ecoregions and provinces. At the ecoregion scale, species are diverse in the north (Cortezian ecoregion) and south (Panama Bight ecoregion) and between insular and coastal ecoregions. At the province scale, we found that the species turnover between the warm temperate Northeast Pacific (WTNP), Tropical East Pacific (TEaP) and the Galapagos Islands (Gala) was high, and the species nestedness was low. At the ecoregion scale, historical factors, and phylogenetic factors have influenced the hotspots of gobiid fish biodiversity, particularly in the Cortezian, Panama Bight and Cocos Island ecoregions, where species turnover is high across both latitudinal and longitudinal gradients. At the provincial level, we found that the contributions of the β-diversity from north to south, in the WTNP, TEaP and Gala were high, as result of the high number of unique species. Species turnover was also high at this scale, with a low contribution from species nestedness that was probably due to the low species/gene flow within the provinces. These results highlight the importance and successful inclusion of a cryptobenthic fish component in ecological and biogeographical studies. © 2018 Valencia-Méndez et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Article, biodiversity, biogeographic region, biogeography, gene flow, goby fish, nonhuman, phylogeny, species distribution, species diversity, taxonomic identification, teleost, animal, animal dispersal, fish, Pacific Ocean, phylogeography, Animal Di CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CIENCIAS AGRARIAS PECES Y FAUNA SILVESTRE PECES Y FAUNA SILVESTRE

Do marine reserves increase prey for California sea lions and Pacific harbor seals?

ALEJANDRO ARIAS DEL RAZO (2019, [Artículo])

Community marine reserves are geographical areas closed to fishing activities, implemented and enforced by the same fishermen that fish around them. Their main objective is to recover commercial stocks of fish and invertebrates. While marine reserves have proven successful in many parts of the world, their success near important marine predator colonies, such as the California sea lion (Zalophus californianus) and the Pacific harbor seal (Phoca vitulina richardii), is yet to be analyzed. In response to the concerns expressed by local fishermen about the impact of the presence of pinnipeds on their communities’ marine reserves, we conducted underwater surveys around four islands in the Pacific west of the Baja California Peninsula: two without reserves (Todos Santos and San Roque); one with a recently established reserve (San Jeronimo); and, a fourth with reserves established eight years ago (Natividad). All these islands are subject to similar rates of exploitation by fishing cooperatives with exclusive rights. We estimated fish biomass and biodiversity in the seas around the islands, applying filters for potential California sea lion and harbor seal prey using known species from the literature. Generalized linear mixed models revealed that the age of the reserve has a significant positive effect on fish biomass, while the site (inside or outside of the reserve) did not, with a similar result found for the biomass of the prey of the California sea lion. Fish biodiversity was also higher around Natividad Island, while invertebrate biodiversity was higher around San Roque. These findings indicate that marine reserves increase overall fish diversity and biomass, despite the presence of top predators, even increasing the numbers of their potential prey. Community marine reserves may help to improve the resilience of marine mammals to climate-driven phenomena and maintain a healthy marine ecosystem for the benefit of both pinnipeds and fishermen. © 2019 Arias-Del-Razo et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Article, biodiversity, biomass, climate change, ecosystem resilience, environmental exploitation, fish stock, fishing, marine environment, marine invertebrate, nonhuman, Phoca vitulina, Pinnipedia, prey searching, Zalophus californianus, animal, biom BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA ANIMAL (ZOOLOGÍA) BIOLOGÍA ANIMAL (ZOOLOGÍA)

Waterhole detection using a vegetation index in desert bighorn sheep (Ovis canadensis cremnobates) habitat

Jonathan Gabriel Escobar Flores (2019, [Artículo])

In arid ecosystems, desert bighorn sheep are dependent on natural waterholes, particularly in summer when forage is scarce and environmental temperatures are high. To detect waterholes in Sierra Santa Isabel, which is the largest area of desert bighorn sheep habitat in the state of Baja California, Mexico, we used the normalized difference vegetation index (NDVI) and normalized difference water index (NDWI) from Sentinel-2 satellite images. Waterhole detection was based on the premise that sites with greater water availability, where NDVI was higher, can be identified by their density of vegetation greenness. For the detected waterholes, we estimated the escape terrain (presence of cliffs or steep, rocky slopes) around each by the vector ruggedness measure to determine their potential use by desert bighorn sheep based on the animals’ presence as documented by camera traps. We detected 14 waterholes with the NDVI of which 11 were known by land owners and 3 were unrecorded. Desert bighorn were not detected in waterholes with high values of escape terrain, i.e., flat areas. Waterhole detection by NDVI is a simple method, and with the assistance and knowledge of the inhabitants of the Sierra, it was possible to confirm the presence each waterhole in the field. © 2019 Escobar-Flores et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Article, bighorn sheep, environmental aspects and related phenomena, environmental parameters, habitat, Mexico, nonhuman, normalized difference vegetation index, normalized difference water index, water availability, waterhole, animal, bighorn sheep, CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CIENCIAS AGRARIAS CIENCIA FORESTAL CIENCIA FORESTAL