Diversity

17 pages, 1304 KiB

Open AccessArticle

Bacterial Communities from Extreme Environments: Vulcano Island

by Camilla Fagorzi, Sara Del Duca, Stefania Venturi, Carolina Chiellini, Giovanni Bacci, Renato Fani and Franco Tassi

Diversity 2019, 11(8), 140; https://doi.org/10.3390/d11080140 - 20 Aug 2019

Cited by 10 | Viewed by 4111

Abstract

Although volcanoes represent extreme environments for life, they harbour bacterial communities. Vulcano Island (Aeolian Islands, Sicily) presents an intense fumarolic activity and widespread soil degassing, fed by variable amounts of magmatic gases (dominant at La Fossa Crater) and hydrothermal fluids (dominant at Levante [...] Read more.

Although volcanoes represent extreme environments for life, they harbour bacterial communities. Vulcano Island (Aeolian Islands, Sicily) presents an intense fumarolic activity and widespread soil degassing, fed by variable amounts of magmatic gases (dominant at La Fossa Crater) and hydrothermal fluids (dominant at Levante Bay). The aim of this study is to analyse the microbial communities from the different environments of Vulcano Island and to evaluate their possible correlation with the composition of the gas emissions. Microbial analyses were carried out on soils and pioneer plants from both La Fossa Crater and Levante Bay. Total DNA has been extracted from all the samples and sequenced through Illumina MiSeq platform. The analysis of microbiome composition and the gases sampled in the same sites could suggest a possible correlation between the two parameters. We can suggest that the ability of different bacterial genera/species to survive in the same area might be due to the selection of particular genetic traits allowing the survival of these microorganisms. On the other side, the finding that microbial communities inhabiting different sites exhibiting different emission profiles are similar might be explained on the basis of a possible sharing of metabolic abilities related to the gas composition. Full article

(This article belongs to the Special Issue Microbial Diversity in Extreme Environments: Implications for Ecological and Applicative Perspectives)

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15 pages, 1546 KiB

Open AccessArticle

Actinobacteria from Extreme Niches in Morocco and Their Plant Growth-Promoting Potentials

by Ahmed Nafis, Anas Raklami, Noura Bechtaoui, Fatima El Khalloufi, Abdelkhalek El Alaoui, Bernard R. Glick, Mohamed Hafidi, Lamfeddal Kouisni, Yedir Ouhdouch and Lahcen Hassani

Diversity 2019, 11(8), 139; https://doi.org/10.3390/d11080139 - 20 Aug 2019

Cited by 60 | Viewed by 6138

Abstract

The objectives of this study were to assess actinobacterial diversity in five Moroccan extreme habitats and to evaluate their plant growth-promoting (PGP) activities. The soil samples were collected from different locations, including soils contaminated with heavy metals, from a high altitude site, from [...] Read more.

The objectives of this study were to assess actinobacterial diversity in five Moroccan extreme habitats and to evaluate their plant growth-promoting (PGP) activities. The soil samples were collected from different locations, including soils contaminated with heavy metals, from a high altitude site, from the desert, and from a marine environment. In total, 23 actinobacteria were isolated, 8 from Merzouga sand soil; 5 from Cannabis sativa rhizospheric soil; 5 from Toubkal mountain; 4 from a Draa sfar mining site; and 1 from marine soil. Based on their genotypic classification using 16S rRNA gene sequences, 19 of all belonged to the genus Streptomyces (82%) while the rest are the members of the genera Nocardioides (4.5%), Saccharomonospora (4.5%), Actinomadura (4.5%), and Prauserella (4.5%). Isolates Streptomyces sp. TNC-1 and Streptomyces sp. MNC-1 showed the highest level of phosphorus solubilization activity with 12.39 and 8.56 mg/mL, respectively. All 23 isolates were able to solubilize potassium, and 91% of them could grow under nitrogen-free conditions. The ability of the isolated actinobacteria to form indole-3-acetic acid (IAA) ranged from 6.70 to 75.54 μg/mL with Streptomyces sp. MNC-1 being the best IAA producer. In addition, all of the actinobacteria could produce siderophores, with Saccharomonospora sp. LNS-1 synthesizing the greatest amount (138.92 μg/mL). Principal coordinate analysis revealed that Streptomyces spp. MNC-1, MNT-1, MNB-2, and KNC-5; Saccharomonospora sp. LNS-1; and Nocardioides sp. KNC-3 each showed a variety of high-level plant growth-promoting activities. The extreme environments in Morocco are rich with bioactive actinobacteria that possess a variety of plant growth-promoting potentials that can further benefit green and sustainable agriculture. Full article

(This article belongs to the Special Issue Microbial Diversity in Extreme Environments: Implications for Ecological and Applicative Perspectives)

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22 pages, 509 KiB

Open AccessReview

A Review of the Effects of Climate Change on Chelonians

by Christopher J. Butler

Diversity 2019, 11(8), 138; https://doi.org/10.3390/d11080138 - 16 Aug 2019

Cited by 31 | Viewed by 10727

Abstract

Climate change is occurring at an unprecedented rate and has begun to modify the distribution and phenology of organisms worldwide. Chelonians are expected to be particularly vulnerable due to limited dispersal capabilities as well as widespread temperature-dependent sex determination. The number of papers [...] Read more.

Climate change is occurring at an unprecedented rate and has begun to modify the distribution and phenology of organisms worldwide. Chelonians are expected to be particularly vulnerable due to limited dispersal capabilities as well as widespread temperature-dependent sex determination. The number of papers published about the effects of climate change on turtles has increased exponentially over the last decade; here, I review the data from peer-reviewed publications to assess the likely impacts of climate change on individuals, populations, and communities. Based upon these studies future research should focus on: (1) Individual responses to climate change, particularly with respect to thermal biology, phenology, and microhabitat selection; (2) improving species distribution models by incorporating fine-scale environmental variables as well as physiological processes; (3) identifying the consequences of skewed sex ratios; and (4) assessments of community resilience and the development of methods to mitigate climate change impacts. Although detailed management recommendations are not possible at this point, careful consideration should be given regarding how to manage low vagility species as habitats shift poleward. In the worst-case scenario, proactive management may be required in order to ensure that widespread losses do not occur. Full article

(This article belongs to the Special Issue Advances in the Biology and Conservation of Turtles)

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13 pages, 12885 KiB

Open AccessArticle

Biotic and Abiotic Factors Affecting the Population Dynamics of Ceratium hirundinella, Peridinium cinctum, and Peridiniopsis elpatiewskyi

by Behrouz Zarei Darki and Alexandr F. Krakhmalnyi

Diversity 2019, 11(8), 137; https://doi.org/10.3390/d11080137 - 15 Aug 2019

Cited by 8 | Viewed by 7247

Abstract

The present research was conducted to assess the impact of abiotic and biotic factors on the growth of freshwater dinoflagellates such as Ceratium hirundinella, Peridinium cinctum, and Peridiniopsis elpatiewskyi, which reduce the quality of drinking water in the Zayandeh Rud [...] Read more.

The present research was conducted to assess the impact of abiotic and biotic factors on the growth of freshwater dinoflagellates such as Ceratium hirundinella, Peridinium cinctum, and Peridiniopsis elpatiewskyi, which reduce the quality of drinking water in the Zayandeh Rud Reservoir. To this end, 152 algal and zoological samples were collected from the reservoir located in the Central part of Iran in January, April, July, and October 2011. Abiotic factors such as pH, temperature, conductivity, transparency, dissolved oxygen, and nutrient concentration of the water were measured in all study stations. The results showed that the population dynamics of dinoflagellates in the Zayandeh Rud Reservoir was different depending on season, station, and depth. The findings proved that C. hirundinella was one of the dominant autumn planktons in the highest biovolume in the Zayandeh Rud Reservoir. While P. elpatiewskyi was present in the reservoir throughout a year with biovolume peak in summer. Accompanying bloom of P. elpatiewskyi and C. hirundinella, P. cinctum also grew in well-heated summer and autumn waters. It was further found that Ceratium density was positively correlated with sulfate ion concentrations, while the growth of P. cinctum and P. elpatiewskyi were associated, first and foremost, with NO₂⁻ and Mn. Full article

(This article belongs to the Special Issue Freshwater Algal Diversity and Bio-Indication of Water Resources)

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22 pages, 5944 KiB

Open AccessArticle

Phytoplankton Blooms, Red Tides and Mucilaginous Aggregates in the Urban Thessaloniki Bay, Eastern Mediterranean

by Savvas Genitsaris, Natassa Stefanidou, Ulrich Sommer and Maria Moustaka-Gouni

Diversity 2019, 11(8), 136; https://doi.org/10.3390/d11080136 - 14 Aug 2019

Cited by 36 | Viewed by 6633

Abstract

We investigated the plankton community composition and abundance in the urban marine environment of Thessaloniki Bay. We collected water samples weekly from March 2017 to February 2018 at the coastal front of Thessaloniki city center and monthly samples from three other inshore sites [...] Read more.

We investigated the plankton community composition and abundance in the urban marine environment of Thessaloniki Bay. We collected water samples weekly from March 2017 to February 2018 at the coastal front of Thessaloniki city center and monthly samples from three other inshore sites along the urban front of the bay. During the study period, conspicuous and successive phytoplankton blooms, dominated by known mucilage-producing diatoms alternated with red tide events formed by the dinoflagellates Noctiluca scintillans and Spatulodinium pseudonoctiluca, and an extensive mucilage aggregate phenomenon, which appeared in late June 2017. At least 11 known harmful algae were identified throughout the study, with the increase in the abundance of the known harmful dinoflagellate Dinophysis cf. acuminata occurring in October and November 2017. Finally, a red tide caused by the photosynthetic ciliate Mesodinium rubrum on December 2017 was conspicuous throughout the sampling sites. The above-mentioned harmful blooms and red tides were linked to high nutrient concentrations and eutrophication. This paper provides an overview of eutrophication impacts on the response of the unicellular eukaryotic plankton organisms and their impact on water quality and ecosystem services. Full article

(This article belongs to the Special Issue Biodiversity of Marine Microbes)

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15 pages, 2604 KiB

Open AccessArticle

Genetic Diversity and Population Structure of Bermudagrass [Cynodon dactylon (L.) Pers.] along Latitudinal Gradients and the Relationship with Polyploidy Level

by Jingxue Zhang, Miaoli Wang, Zhipeng Guo, Yongzhuo Guan, Jianyu Liu, Xuebing Yan and Yuxia Guo

Diversity 2019, 11(8), 135; https://doi.org/10.3390/d11080135 - 14 Aug 2019

Cited by 14 | Viewed by 4191

Abstract

Understanding the population genetic pattern and process of gene flow requires a detailed knowledge of how landscape characteristics structure populations. Although Cynodon dactylon (L.) Pers. (common bermudagrass) is widely distributed in the world, information on its genetic pattern and population structure along latitudinal [...] Read more.

Understanding the population genetic pattern and process of gene flow requires a detailed knowledge of how landscape characteristics structure populations. Although Cynodon dactylon (L.) Pers. (common bermudagrass) is widely distributed in the world, information on its genetic pattern and population structure along latitudinal gradients is limited. We tried to estimate the genetic diversity and genetic structure of C. dactylon along a latitudinal gradient across China. Genetic diversity among different ploidy levels was also compared in the study. The material used consisted of 296 C. dactylon individuals sampled from 16 geographic sites from 22°35′ N to 36°18′ N. Genetic diversity was estimated using 153 expressed sequence tag-derived simple sequence repeat (EST-SSR) loci. Higher within-population genetic diversity appeared at low-latitude, as well as having positive correlation with temperature and precipitation. The genetic diversity increased with the ploidy level of C. dactylon, suggesting polyploidy creates higher genetic diversity. No isolation by distance and notable admixture structure existed among populations along latitudes. Both seed dispersal (or vegetative organs) and extrinsic pollen played important roles for gene flow in shaping the spatial admixture population structure of C. dactylon along latitudes. In addition, populations were separated into three clusters according to ploidy levels. C. dactylon has many such biological characters of perennial growth, wind-pollination, polyploidy, low genetic differentiation among populations, sexual and asexual reproduction leading to higher genetic diversity, which gives it strong adaptability with its genetic patterns being very complex across all the sampled latitudes. The findings of this study are related to landscape population evolution, polyploidy speciation, preservation, and use of bermudagrass breeding. Full article

(This article belongs to the Section Plant Diversity)

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13 pages, 2788 KiB

Open AccessArticle

Invasive Goldenrod (Solidago gigantea) Influences Soil Microbial Activities in Forest and Grassland Ecosystems in Central Europe

by Lenka Bobuľská, Lenka Demková, Andrea Čerevková and Marek Renčo

Diversity 2019, 11(8), 134; https://doi.org/10.3390/d11080134 - 14 Aug 2019

Cited by 14 | Viewed by 3430

Abstract

A giant goldenrod plant, Solidago gigantea, native to North America is rapidly spreading in Europe and may have serious impact on ecosystems that inhabit. There is a lack of information about the effects of this species on soil biochemical properties and distribution [...] Read more.

A giant goldenrod plant, Solidago gigantea, native to North America is rapidly spreading in Europe and may have serious impact on ecosystems that inhabit. There is a lack of information about the effects of this species on soil biochemical properties and distribution and activity of microbial community. We analyzed soil physicochemical properties (soil reaction, soil moisture content, organic carbon and total nitrogen content) associated with activity of microbial population (activity of fluorescein diacetate (FDA), beta-glucosidase, urease and phosphatases enzymes) between invaded and adjacent uninvaded control sites in two habitats, forest and grassland, in the lowland of southeast Slovakia during years 2016 and 2017. The results revealed that invasion of S. gigantea significantly altered several soil properties and is associated with different soil properties. Soil acidity increased, organic carbon and moisture content decreased, while total nitrogen content was not significantly affected by invasion. FDA and urease activity were significantly higher in uninvaded sites. In contrast, beta-glucosidase and alkaline phosphatase activity were enhanced by S. gigantea invasion in both ecosystems studied. Acid phosphatase was not affected by the invasion. Our study proved that S. gigantea can influence several soil microbial properties while others remained unaffected, despite its significant impact on basal soil physicochemical properties. Full article

(This article belongs to the Section Plant Diversity)

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20 pages, 2027 KiB

Open AccessArticle

Cross Taxon Congruence Between Lichens and Vascular Plants in a Riparian Ecosystem

by Giovanni Bacaro, Enrico Tordoni, Stefano Martellos, Simona Maccherini, Michela Marignani, Lucia Muggia, Francesco Petruzzellis, Rossella Napolitano, Daniele Da Re, Tommaso Guidi, Renato Benesperi, Vincenzo Gonnelli and Lorenzo Lastrucci

Diversity 2019, 11(8), 133; https://doi.org/10.3390/d11080133 - 13 Aug 2019

Cited by 7 | Viewed by 3610

Abstract

Despite that congruence across taxa has been proved as an effective tool to provide insights into the processes structuring the spatial distribution of taxonomic groups and is useful for conservation purposes, only a few studies on cross-taxon congruence focused on freshwater ecosystems and [...] Read more.

Despite that congruence across taxa has been proved as an effective tool to provide insights into the processes structuring the spatial distribution of taxonomic groups and is useful for conservation purposes, only a few studies on cross-taxon congruence focused on freshwater ecosystems and on the relations among vascular plants and lichens. We hypothesized here that, since vascular plants could be good surrogates of lichens in these ecosystems, it would be possible to assess the overall biodiversity of riparian habitats using plant data only. In this frame, we explored the relationship between (a) species richness and (b) community composition of plants and lichens in a wetland area located in central Italy to (i) assess whether vascular plants are good surrogates of lichens and (ii) to test the congruence of patterns of species richness and composition among plants and lichens along an ecological gradient. The general performance of plant species richness per se, as a biodiversity surrogate of lichens, had poor results. Nonetheless, the congruence in compositional patterns between lichens and vascular plants varied across habitats and was influenced by the characteristics of the vegetation. In general, we discussed how the strength of the studied relationships could be influenced by characteristics of the data (presence/absence vs. abundance), by the spatial scale, and by the features of the habitats. Overall, our data confirm that the more diverse and structurally complex the vegetation is, the more diverse are the lichen communities it hosts. Full article

(This article belongs to the Special Issue Lichen Diversity and Biomonitoring)

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26 pages, 3979 KiB

Open AccessArticle

Dactylogyrids (Platyhelminthes: Monogenoidea) Infecting the Gill Lamellae of Flatheads (Scorpaeniformes: Platycephalidae), with Proposal of Platycephalotrema n. gen. and Descriptions of New Species from Australia and Japan

by Delane C. Kritsky and Masato Nitta

Diversity 2019, 11(8), 132; https://doi.org/10.3390/d11080132 - 12 Aug 2019

Cited by 9 | Viewed by 3339

Abstract

Platycephalotrema n. gen. (Dactylogyridae) is proposed for four new species and 5 previously described species parasitizing the gills of flatheads (Scorpaeniformes: Platycephalidae) as follows: Platycephalotrema ogawai n. sp. (type species) from Platycephalus sp. 1 (type host) and Platycephalus sp. 2, both of Nakabo [...] Read more.

Platycephalotrema n. gen. (Dactylogyridae) is proposed for four new species and 5 previously described species parasitizing the gills of flatheads (Scorpaeniformes: Platycephalidae) as follows: Platycephalotrema ogawai n. sp. (type species) from Platycephalus sp. 1 (type host) and Platycephalus sp. 2, both of Nakabo & Kai (2013) (locally known as “Yoshino-gochi” and “Ma-gochi,” respectively) (Japan); Platycephalotrema austrinum n. sp. from Platycephalus endrachtensis Quoy & Gaimard (type host) and Platycephalus sp. (Australia); Platycephalotrema bassensis (Hughes, 1928) n. comb. from Platycephalus bassensis Cuvier (Australia); Platycephalotrema koppa n. sp. from Platycephalus fuscus Cuvier (Australia); Platycephalotrema macassarensis (Yamaguti, 1963) n. comb. from Platycephalus indicus (Linnaeus) (China, Macassar); Platycephalotrema mastix n. sp. from P. fuscus and P. endrachtensis (Australia); Platycephalotrema platycephali (Yin & Sproston, 1948) n. comb. from P. indicus (China) and P. fuscus (Australia); Platycephalotrema sinensis (Yamaguti, 1963) n. comb. from Cociella punctata (Cuvier) (China); Platycephalotrema thysanophrydis (Yamaguti, 1937) n. comb. from Inegocia japonica (Cuvier), Inegocia ochiaii Imamura, and Cociella crocodilus (Cuvier) (Japan, China). Other species requiring further study but potentially members of Platycephalotrema include Ancyrocephalus vesiculosus Murray, 1931, Haliotrema indicum Tripathi, 1957, Haliotrema swatowensis Yao, Wang, Xia, & Chen, 1998, and Haliotrema pteroisi Paperna, 1972. The primary features differentiating Platycephalotrema include species having: (1) tandem gonads (testis postgermarial); (2) two prostatic reservoirs, each emptying independently into the base of the male copulatory organ; (3) a dextral vaginal pore and large vaginal vestibule; (4) dorsal and ventral pairs of morphologically similar anchors; (5) a ventral bar with spatulate ends; (6) a dorsal bar with bifurcated ends, and (7) absence of an accessory piece. The new species are described, and P. thysanophrydis is redescribed based on newly collected and museum specimens. Full article

(This article belongs to the Special Issue Taxonomy and Diversity of Aquaculture and Fisheries Parasites)

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25 pages, 2515 KiB

Open AccessArticle

The Vertebrate TLR Supergene Family Evolved Dynamically by Gene Gain/Loss and Positive Selection Revealing a Host–Pathogen Arms Race in Birds

by Imran Khan, Emanuel Maldonado, Liliana Silva, Daniela Almeida, Warren E. Johnson, Stephen J. O’Brien, Guojie Zhang, Erich D. Jarvis, M. Thomas P. Gilbert and Agostinho Antunes

Diversity 2019, 11(8), 131; https://doi.org/10.3390/d11080131 - 12 Aug 2019

Cited by 22 | Viewed by 6299

Abstract

The vertebrate toll-like receptor (TLRs) supergene family is a first-line immune defense against viral and non-viral pathogens. Here, comparative evolutionary-genomics of 79 vertebrate species (8 mammals, 48 birds, 11 reptiles, 1 amphibian, and 11 fishes) revealed differential gain/loss of 26 TLRs, including 6 [...] Read more.

The vertebrate toll-like receptor (TLRs) supergene family is a first-line immune defense against viral and non-viral pathogens. Here, comparative evolutionary-genomics of 79 vertebrate species (8 mammals, 48 birds, 11 reptiles, 1 amphibian, and 11 fishes) revealed differential gain/loss of 26 TLRs, including 6 (TLR3, TLR7, TLR8, TLR14, TLR21, and TLR22) that originated early in vertebrate evolution before the diversification of Agnatha and Gnathostomata. Subsequent dynamic gene gain/loss led to lineage-specific diversification with TLR repertoires ranging from 8 subfamilies in birds to 20 in fishes. Lineage-specific loss of TLR8-9 and TLR13 in birds and gains of TLR6 and TLR10-12 in mammals and TLR19-20 and TLR23-27 in fishes. Among avian species, 5–10% of the sites were under positive selection (PS) (omega 1.5–2.5) with radical amino-acid changes likely affecting TLR structure/functionality. In non-viral TLR4 the 20 PS sites (posterior probability PP > 0.99) likely increased ability to cope with diversified ligands (e.g., lipopolysaccharide and lipoteichoic). For viral TLR7, 23 PS sites (PP > 0.99) possibly improved recognition of highly variable viral ssRNAs. Rapid evolution of the TLR supergene family reflects the host–pathogen arms race and the coevolution of ligands/receptors, which follows the premise that birds have been important vectors of zoonotic pathogens and reservoirs for viruses. Full article

(This article belongs to the Special Issue Genomic Analyses of Avian Evolution)

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10 pages, 3264 KiB

Open AccessReview

Immediate Effects of Hurricanes on a Diverse Coral/Mangrove Ecosystem in the U.S. Virgin Islands and the Potential for Recovery

by Caroline S. Rogers

Diversity 2019, 11(8), 130; https://doi.org/10.3390/d11080130 - 12 Aug 2019

Cited by 13 | Viewed by 5755

Abstract

Hurricanes Irma and Maria, two powerful storms that hit the U.S. Virgin Islands less than 2 weeks apart in September 2017, caused extensive damage to the natural resources on St. John. Damage was particularly severe in a unique mangrove/coral ecosystem in three bays [...] Read more.

Hurricanes Irma and Maria, two powerful storms that hit the U.S. Virgin Islands less than 2 weeks apart in September 2017, caused extensive damage to the natural resources on St. John. Damage was particularly severe in a unique mangrove/coral ecosystem in three bays within Virgin Islands Coral Reef National Monument, a National Park Service marine protected area. Many Red Mangrove (Rhizophora mangle) trees were uprooted and tossed into the sea, and the prop roots of others were stripped of corals, sponges and other marine life. No other mangrove area in the Caribbean is known to have so many scleractinian corals (about 30 species before the storms). Although many corals were overturned or buried in rubble, colonies of most of the species, including four that are listed as threatened under the U.S. Endangered Species Act, survived. Recovery of this ecosystem will depend on Red Mangrove propagules becoming established and producing prop roots to support rich marine life along with a canopy to provide the shade that was critical to the biodiversity that was present before the storms. Unlike in many situations where major disturbances reduce coral cover, the substrate that must be restored for full recovery to occur is a living substrate—the prop roots of the mangroves. Larvae of corals and sponges will need to recruit on to the roots. Future storms could hinder this process. Full article

(This article belongs to the Special Issue Review Papers on Marine Diversity)

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20 pages, 2355 KiB

Open AccessArticle

Endemic Infection of Batrachochytrium dendrobatidis in Costa Rica: Implications for Amphibian Conservation at Regional and Species Level

by Héctor Zumbado-Ulate, Kiersten N. Nelson, Adrián García-Rodríguez, Gerardo Chaves, Erick Arias, Federico Bolaños, Steven M. Whitfield and Catherine L. Searle

Diversity 2019, 11(8), 129; https://doi.org/10.3390/d11080129 - 09 Aug 2019

Cited by 16 | Viewed by 7001

Abstract

Batrachochytrium dendrobatidis (Bd) has been associated with the severe declines and extinctions of amphibians in Costa Rica that primarily occurred during the 1980s and 1990s. However, the current impact of Bd infection on amphibian species in Costa Rica is unknown. We [...] Read more.

Batrachochytrium dendrobatidis (Bd) has been associated with the severe declines and extinctions of amphibians in Costa Rica that primarily occurred during the 1980s and 1990s. However, the current impact of Bd infection on amphibian species in Costa Rica is unknown. We aimed to update the list of amphibian species in Costa Rica and evaluate the prevalence and infection intensity of Bd infection across the country to aid in the development of effective conservation strategies for amphibians. We reviewed taxonomic lists and included new species descriptions and records for a total of 215 amphibian species in Costa Rica. We also sampled for Bd at nine localities from 2015–2018 and combined these data with additional Bd occurrence data from multiple studies conducted in amphibian communities across Costa Rica from 2005–2018. With this combined dataset, we found that Bd was common (overall infection rate of 23%) across regions and elevations, but infection intensity was below theoretical thresholds associated with mortality. Bd was also more prevalent in Caribbean lowlands and in terrestrial amphibians with an aquatic larval stage; meanwhile, infection load was the highest in direct-developing species (forest and stream-dwellers). Our findings can be used to prioritize regions and taxonomic groups for conservation strategies. Full article

(This article belongs to the Special Issue Systematics and Conservation of Neotropical Amphibians and Reptiles)

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23 pages, 2532 KiB

Open AccessReview

Parageobacillus thermantarcticus, an Antarctic Cell Factory: From Crop Residue Valorization by Green Chemistry to Astrobiology Studies

by Ilaria Finore, Licia Lama, Paola Di Donato, Ida Romano, Annabella Tramice, Luigi Leone, Barbara Nicolaus and Annarita Poli

Diversity 2019, 11(8), 128; https://doi.org/10.3390/d11080128 - 07 Aug 2019

Cited by 11 | Viewed by 4606

Abstract

Knowledge of Antarctic habitat biodiversity, both marine and terrestrial, has increased considerably in recent years, causing considerable development in the studies of life science related to Antarctica. In the Austral summer 1986–1987, a new thermophilic bacterium, Parageobacillus thermantarcticus strain M1 was isolated from [...] Read more.

Knowledge of Antarctic habitat biodiversity, both marine and terrestrial, has increased considerably in recent years, causing considerable development in the studies of life science related to Antarctica. In the Austral summer 1986–1987, a new thermophilic bacterium, Parageobacillus thermantarcticus strain M1 was isolated from geothermal soil of the crater of Mount Melbourne (74°22′ S, 164°40′ E) during the Italian Antarctic Expedition. In addition to the biotechnological potential due to the production of exopolysaccharides and thermostable enzymes, successful studies have demonstrated its use in the green chemistry for the transformation and valorization of residual biomass and its employment as a suitable microbial model for astrobiology studies. The recent acquisition of its genome sequence opens up new opportunities for the use of this versatile bacterium in still unexplored biotechnology sectors. Full article

(This article belongs to the Special Issue Microbial Diversity in Extreme Environments: Implications for Ecological and Applicative Perspectives)

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28 pages, 1000 KiB

Open AccessArticle

A Comparison of Systematic Quadrat and Capture-Mark-Recapture Sampling Designs for Assessing Freshwater Mussel Populations

by Caitlin S. Carey, Jess W. Jones, Robert S. Butler, Marcella J. Kelly and Eric M. Hallerman

Diversity 2019, 11(8), 127; https://doi.org/10.3390/d11080127 - 07 Aug 2019

Cited by 4 | Viewed by 4652

Abstract

Our study objective was to compare the relative effectiveness and efficiency of quadrat and capture-mark-recapture (CMR) sampling designs for monitoring mussels. We collected data on a recently reintroduced population of federally endangered Epioblasma capsaeformis and two nonlisted, naturally occurring species—Actinonaias pectorosa and [...] Read more.

Our study objective was to compare the relative effectiveness and efficiency of quadrat and capture-mark-recapture (CMR) sampling designs for monitoring mussels. We collected data on a recently reintroduced population of federally endangered Epioblasma capsaeformis and two nonlisted, naturally occurring species—Actinonaias pectorosa and Medionidus conradicus—in the Upper Clinch River, Virginia, over two years using systematic quadrat and CMR sampling. Both sampling approaches produced similar estimates of abundance; however, precision of estimates varied between approaches, years, and among species, and further, quadrat sampling efficiency of mussels detectable on the substrate surface varied among species. CMR modeling revealed that capture probabilities for all three study species varied by time and were positively associated with shell length, that E. capsaeformis detection was influenced by sex, and that year-to-year apparent survival was high (>96%) for reintroduced E. capsaeformis. We recommend that monitoring projects use systematic quadrat sampling when the objective is to estimate and detect trends in abundance for species of moderate to high densities (>0.2/m²), whereas a CMR component should be incorporated when objectives include assessing reintroduced populations, obtaining reliable estimates of survival and recruitment, or producing unbiased population estimates for species of low to moderate densities (≤0.2/m²). Full article

(This article belongs to the Special Issue Aquatic Environmental Monitoring and Assessment)

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14 pages, 2046 KiB

Open AccessArticle

Phylogenomic Reconstruction of the Neotropical Poison Frogs (Dendrobatidae) and Their Conservation

by Wilson X. Guillory, Morgan R. Muell, Kyle Summers and Jason L. Brown

Diversity 2019, 11(8), 126; https://doi.org/10.3390/d11080126 - 29 Jul 2019

Cited by 22 | Viewed by 17865

Abstract

The evolutionary history of the Dendrobatidae, the charismatic Neotropical poison frog family, remains in flux, even after a half-century of intensive research. Understanding the evolutionary relationships between dendrobatid genera and the larger-order groups within Dendrobatidae is critical for making accurate assessments of all [...] Read more.

The evolutionary history of the Dendrobatidae, the charismatic Neotropical poison frog family, remains in flux, even after a half-century of intensive research. Understanding the evolutionary relationships between dendrobatid genera and the larger-order groups within Dendrobatidae is critical for making accurate assessments of all aspects of their biology and evolution. In this study, we provide the first phylogenomic reconstruction of Dendrobatidae with genome-wide nuclear markers known as ultraconserved elements. We performed sequence capture on 61 samples representing 33 species across 13 of the 16 dendrobatid genera, aiming for a broadly representative taxon sample. We compare topologies generated using maximum likelihood and coalescent methods and estimate divergence times using Bayesian methods. We find most of our dendrobatid tree to be consistent with previously published results based on mitochondrial and low-count nuclear data, with notable exceptions regarding the placement of Hyloxalinae and certain genera within Dendrobatinae. We also characterize how the evolutionary history and geographic distributions of the 285 poison frog species impact their conservation status. We hope that our phylogeny will serve as a backbone for future evolutionary studies and that our characterizations of conservation status inform conservation practices while highlighting taxa in need of further study. Full article

(This article belongs to the Special Issue Systematics and Conservation of Neotropical Amphibians and Reptiles)

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13 pages, 987 KiB

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Willow Short-Rotation Coppice as Model System for Exploring Ecological Theory on Biodiversity–Ecosystem Function

by Martin Weih, Carolyn Glynn and Christel Baum

Diversity 2019, 11(8), 125; https://doi.org/10.3390/d11080125 - 29 Jul 2019

Cited by 15 | Viewed by 6177

Abstract

Plantations of willow (Salix spp.) are today grown as short-rotation coppice (SRC) for the sustainable production of biomass. While developing these production systems in the past, much ecological knowledge on plant–plant, plant–environment and trophic interactions has been generated. This knowledge can contribute [...] Read more.

Plantations of willow (Salix spp.) are today grown as short-rotation coppice (SRC) for the sustainable production of biomass. While developing these production systems in the past, much ecological knowledge on plant–plant, plant–environment and trophic interactions has been generated. This knowledge can contribute to the further development of biodiversity–ecosystem function (BEF) theory, which frequently lacks a sound understanding of the complex mechanisms behind the observed patterns of diversity-productivity relationships. Thus, willow SRC systems are suitable models to explore BEF theory; they are simple enough to allow the study of the complex ecological mechanisms involved and they have many similarities to grassland systems in which much of recent BEF theory development has been achieved. This paper briefly reviews the current observational and mechanistic knowledge on diversity–productivity relationships in willow SRC, as well as the most important above- and below-ground trophic interactions that are likely to affect them. If the available knowledge is integrated and combined with further experimental work targeting mechanisms behind patterns, research on willow SRC as a model offers a great opportunity for filling the gaps in the understanding what presently hampers the development of predictive BEF theory. Full article

(This article belongs to the Special Issue Biodiversity of Short Rotation Willow and Perennial Rhizomatous Grass Crops)

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22 pages, 69074 KiB

Open AccessArticle

Movement and Home Range of the Smooth Softshell Turtle (Apalone mutica): Spatial Ecology of a River Specialist

by Jason P. Ross, Robert D. Bluett and Michael J. Dreslik

Diversity 2019, 11(8), 124; https://doi.org/10.3390/d11080124 - 26 Jul 2019

Cited by 6 | Viewed by 5338

Abstract

Spatial ecological information is necessary to guide the conservation efforts of river turtles, but it is lacking for many species including the smooth softshell turtle (Apalone mutica). We investigated the spatial ecology of A. mutica in two reaches of the Kaskaskia [...] Read more.

Spatial ecological information is necessary to guide the conservation efforts of river turtles, but it is lacking for many species including the smooth softshell turtle (Apalone mutica). We investigated the spatial ecology of A. mutica in two reaches of the Kaskaskia River in Illinois, USA to determine variables influencing movement rates, the best estimate of home range, and variables influencing home range size. We radio-tracked 28 A. mutica from 2013 to 2014 and used an information theoretic approach to select the best models describing movement and home range estimates. Mean movement rate was 142.3 m/day and was highly variable with some movements >2 km/day. Movement peaked at moderate water temperatures early in the active season, increased at higher water levels for females, and was greater in the higher stream order. The sexes responded differently to environmental variation, with female movement higher in most but not all conditions. The most informative home range estimate was a 95% kernel density estimate using likelihood cross-validation (CVh) smoothing clipped to the river channel. The mean home range size was 18.1 hectares and increased with movement rate, number of radio-locations, and stream order. Most turtles had well-defined home ranges, though a few were possibly nomadic. Our methods also provide a framework for spatial ecological studies of other riverine species. Full article

(This article belongs to the Special Issue Advances in the Biology and Conservation of Turtles)

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35 pages, 4935 KiB

Open AccessArticle

A Comprehensive Study of Orchid Seed Production Relative to Pollination Traits, Plant Density and Climate in an Urban Reserve in Western Australia

by Mark C. Brundrett

Diversity 2019, 11(8), 123; https://doi.org/10.3390/d11080123 - 26 Jul 2019

Cited by 18 | Viewed by 9632

Abstract

The pollination of 20 common terrestrial orchids was studied in a 60-ha urban banksia and eucalypt dominated woodland in Western Australia. Five years of data (24,000 flowers, 6800 plants) measured fruit set relative to floral areas, capsule volumes, climate, phenology, pollination mechanisms, disturbance [...] Read more.

The pollination of 20 common terrestrial orchids was studied in a 60-ha urban banksia and eucalypt dominated woodland in Western Australia. Five years of data (24,000 flowers, 6800 plants) measured fruit set relative to floral areas, capsule volumes, climate, phenology, pollination mechanisms, disturbance tolerance and demography. Pollination varied from 0–95% of flowers, floral displays from 90–3300 mm² and capsules from 15–1300 mm³ per spike. Pollination traits strongly influenced outcomes, with self-pollination highest (59—95%), followed by sexually deceptive autumn or winter-flowering (18–39%), visual deception (0–48%) and sexually deceptive spring-flowering (13–16%). Pollination was limited by drought in autumn or spring and cool winter temperatures. Some orchids were resilient to drought and one formed seed after the leaves withered. Plant density had the greatest impact on fruit set for orchids forming large groups, especially for sexually deceptive pollination. Consequently, small group average (SGA) pollination was up to 4× greater than overall averages and peak seed production occurred in the best locations for genetic exchange and dispersal. SGA rates and seedpod volumes were strongly linked to clonality, but not to demographic trends. Resource competition limited flowering at higher plant densities and competition within spikes resulted in smaller, later-forming seedpods. Pollination data from co-occurring common orchids identified five evolutionary trade-offs linked to pollination, provided baseline data for rare species and revealed impacts of changing climate. Full article

(This article belongs to the Special Issue The Ecology and Diversity of Orchids)

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16 pages, 2590 KiB

Open AccessArticle

Assessment of Changes in the Structure of Zooplankton Communities to Infer Water Quality of the Caspian Sea

by Elena Krupa

Diversity 2019, 11(8), 122; https://doi.org/10.3390/d11080122 - 26 Jul 2019

Cited by 6 | Viewed by 4779

Abstract

The work aimed to study the structural variables of zooplankton to assess the water quality of the Caspian Sea. Studies of zooplankton were conducted in the spring and summer of 2008 and 2010. Abundance, biomass, an average individual mass of a specimen, Shannon [...] Read more.

The work aimed to study the structural variables of zooplankton to assess the water quality of the Caspian Sea. Studies of zooplankton were conducted in the spring and summer of 2008 and 2010. Abundance, biomass, an average individual mass of a specimen, Shannon Bi, Shannon Ab, Δ-Shannon indices, and Clarke’s W-statistic were calculated for zooplankton. Quantitative variables of zooplankton were the highest in the Northeastern and Northern Caspian, decreasing towards the Middle Caspian. In the Northeastern and Northern Caspian from spring to summer, the number of zooplankton, and the values of Shannon Bi and Shannon Ab indices decreased; the values of Δ-Shannon and Clarke’s W-statistic increased. In the Middle Caspian, the biomass of the community increased; the values of Δ-Shannon and Clarke’s W-statistic decreased. From spring to summer, the value of an average individual mass of a specimen decreased over the entire surveyed area. The jellyfish Blackfordia virginica and Moerisia pallasi significantly influenced the size structure of the holoplankton. Seasonal dynamics of structural variables of zooplankton as well as changes in water transparency showed that water quality improved from spring to summer in the shallow northern and northeastern areas of the sea, and decreased in the deep-water Middle Caspian. Full article

(This article belongs to the Special Issue Freshwater Algal Diversity and Bio-Indication of Water Resources)

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11 pages, 2294 KiB

Open AccessArticle

GIS-modeling of the Range Shifts of the Sub-fossil and Extant European Pond Turtle (Emys orbicularis) in Eastern Europe in Holocene

by Oksana Nekrasova, Yevheniia Yanish, Volodymyr Tytar and Mihails Pupins

Diversity 2019, 11(8), 121; https://doi.org/10.3390/d11080121 - 26 Jul 2019

Cited by 4 | Viewed by 4821

Abstract

The study of the dynamics of the European pond turtle’s Emys orbicularis range and distribution as an indicator of climate change in the past, present, and future is most relevant in connection with the protected status of this species in Europe. Based on [...] Read more.

The study of the dynamics of the European pond turtle’s Emys orbicularis range and distribution as an indicator of climate change in the past, present, and future is most relevant in connection with the protected status of this species in Europe. Based on our original finds, 25 archaeological sites yielding 1623 remains of 1504 individuals of subfossil pond turtles, current marginal distribution in Latvia, Ukraine, Russia, and literature data, we analyzed 437 records of Holocene turtles and 2847 current records of pond turtles. We identified areas that could serve as refugia for E. orbicularis, as a result of GIS modeling, while using 19 bioclimatic variables from the Worldclim and PaleoClim data bases. The data obtained confirm current hypotheses regarding the origin of more than 10 mtDNA lineages of E. orbicularis and the existence of multiple glacial refugia, and considerable Holocene home range dynamics. Full article

(This article belongs to the Special Issue Advances in the Biology and Conservation of Turtles)

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16 pages, 1072 KiB

Open AccessArticle

Living on the Edge: Variation in the Abundance and Demography of a Kelp Forest Epibiont

by Katie K. Arkema and Jameal F. Samhouri

Diversity 2019, 11(8), 120; https://doi.org/10.3390/d11080120 - 26 Jul 2019

Cited by 6 | Viewed by 4066

Abstract

The ecology of an epibiont may depend not only on the dynamics of its biogenic habitat but also on microclimate variation generated within aggregations of its host, a process called physical ecosystem engineering. This study explored variation in the abundance and demography of [...] Read more.

The ecology of an epibiont may depend not only on the dynamics of its biogenic habitat but also on microclimate variation generated within aggregations of its host, a process called physical ecosystem engineering. This study explored variation in the abundance and demography of Membranipora, a suspension-feeding bryozoan, within forests of giant kelp (Macrocystis pyrifera) off the coast of Santa Barbara, California, USA. First, we assessed differences in Membranipora abundance between the edge and interior of kelp forests. The occurrence of Membranipora on kelp blades and its percent cover on occupied blades were higher along forest edges than interiors. Second, we conducted observational studies and field experiments to understand spatial variation in substrate longevity, colony mortality, larval recruitment, and colony growth rates. A higher density of recruits and colonies occurred along forest edges than interiors, suggesting kelp acts like a sieve, whereby larvae settle to edge blades first. Moreover, growth rates along the edge were up to 45% higher than forest interiors. Reduced current speeds, combined with feeding by exterior colonies, may have lowered the uptake of suspended food particles by interior colonies. These results suggest that variation in Membranipora abundance is due in part to differences in colony growth between forest edges and interiors, and not solely the result of recruitment limitation. Our results highlight the importance of ecosystem engineers in influencing the ecological dynamics of epiphytic flora and fauna in marine systems. Full article

(This article belongs to the Special Issue Diversity of Ecosystem Engineers in the World Coasts and Oceans)

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16 pages, 1321 KiB

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Exploring the Interplay Between Local and Regional Drivers of Distribution of a Subterranean Organism

by Stefano Mammola, Shlomi Aharon, Merav Seifan, Yael Lubin and Efrat Gavish-Regev

Diversity 2019, 11(8), 119; https://doi.org/10.3390/d11080119 - 25 Jul 2019

Cited by 9 | Viewed by 4043

Abstract

Caves are excellent model systems to study the effects of abiotic factors on species distributions due to their selective conditions. Different ecological factors have been shown to affect species distribution depending on the scale of analysis, whether regional or local. The interplay between [...] Read more.

Caves are excellent model systems to study the effects of abiotic factors on species distributions due to their selective conditions. Different ecological factors have been shown to affect species distribution depending on the scale of analysis, whether regional or local. The interplay between local and regional factors in explaining the spatial distribution of cave-dwelling organisms is poorly understood. Using the troglophilic subterranean spider Artema nephilit (Araneae: Pholcidae) as a model organism, we investigated whether similar environmental predictors drive the species distribution at these two spatial scales. At the local scale, we monitored the abundance of the spiders and measured relevant environmental features in 33 caves along the Jordan Rift Valley. We then extended the analysis to a regional scale, investigating the drivers of the distribution using species distribution models. We found that similar ecological factors determined the distribution at both local and regional scales for A. nephilit. At a local scale, the species was found to preferentially occupy the outermost, illuminated, and warmer sectors of caves. Similarly, mean annual temperature, annual temperature range, and solar radiation were the most important drivers of its regional distribution. By investigating these two spatial scales simultaneously, we showed that it was possible to achieve an in-depth understanding of the environmental conditions that governs subterranean species distribution. Full article

(This article belongs to the Special Issue Systematics and Evolution of Spiders)

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12 pages, 9187 KiB

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Risks of Mixtures of Oil Sands Contaminants to a Sensitive Mayfly Sentinel, Hexagenia

by Julia Howland, Alexa Alexander, Danielle Milani, Kerry Peru and Joseph Culp

Diversity 2019, 11(8), 118; https://doi.org/10.3390/d11080118 - 24 Jul 2019

Cited by 4 | Viewed by 3232

Abstract

Tailings ponds in northeastern Alberta, Canada contain massive amounts of oil sands process water (OSPW) that cannot currently be released due to the toxicity of some components. Limited space and the need for reclamation of oil sands operation sites will necessitate the release [...] Read more.

Tailings ponds in northeastern Alberta, Canada contain massive amounts of oil sands process water (OSPW) that cannot currently be released due to the toxicity of some components. Limited space and the need for reclamation of oil sands operation sites will necessitate the release of OSPW in the near future. Knowledge of the composition and toxicity of OSPW is lacking yet is crucial for both risk assessment and management planning. This study examines chronic toxicity of a mixture of OSPW components sodium naphthenate and naphthenic acid (NA) to nymphs of the mayfly Hexagenia spp. in control and polycyclic aromatic hydrocarbons (PAH)-spiked sediment treatments. The objective of this study was to determine whether the addition of the PAH-spiked sediment significantly contributed to or masked responses of these sensitive mayflies to mixtures of NA. Mean survival in nymphs exposed to NA and PAH-spiked sediment treatments was reduced by 48% compared to those exposed to the NA mixture alone. Lethal responses were observed in all of the PAH-spiked sediment treatments. However, within PAH-spiked and control sediment treatments, there was no significant difference in nymph survival due to NA concentration, indicating that changes in survivorship were predominantly a reflection of increased mortality associated with sediment PAHs and not to the NA mixture treatment. Sublethal effects on body segment ratios suggest that mayflies exposed to NA and PAH-spiked sediment, as well as those exposed to the highest NA concentration tested (1 mg/L) and control sediment, made developmental trade-offs in order to emerge faster and escape a stressful environment. These results reveal that the release of OSPW to the surrounding environment could cause a reduction in mayfly populations. Mayflies provide ecosystem services and are an important food source for higher trophic levels in both the aquatic and terrestrial communities. Full article

(This article belongs to the Special Issue Aquatic Environmental Monitoring and Assessment)

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Diversity, Volume 11, Issue 8 (August 2019) – 23 articles

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