Association of seropositivity to Helicobacter species and biliary tract cancer in the ATBC study.

PubMed

Murphy, Gwen; Michel, Angelika; Taylor, Philip R; Albanes, Demetrius; Weinstein, Stephanie J; Virtamo, Jarmo; Parisi, Dominick; Snyder, Kirk; Butt, Julia; McGlynn, Katherine A; Koshiol, Jill; Pawlita, Michael; Lai, Gabriel Y; Abnet, Christian C; Dawsey, Sanford M; Freedman, Neal D

2014-12-01

Helicobacter have been detected in human bile and hepatobiliary tissue. Despite evidence that Helicobacter species promote gallstone formation and hepatobiliary tumors in laboratory studies, it remains unclear whether Helicobacter species contribute to these cancers in humans. We used a multiplex panel to assess whether seropositivity to 15 Helicobacter pylori proteins was associated with subsequent incidence of hepatobiliary cancers in the Finnish Alpha-Tocopherol, Beta-Carotene Cancer Prevention (ATBC) Study. We included 64 biliary cancers, 122 liver cancers, and 224 age-matched controls which occurred over the course of 22 years. Helicobacter pylori seropositivity was defined as those positive to ≥ 4 antigens. Odds ratios (OR) and 95% confidence intervals were adjusted for major hepatobiliary cancer risk factors. Among the controls, 88% were seropositive to H. pylori at baseline. Among those who subsequently developed hepatobiliary cancer, the prevalence of seropositivity was higher: 100% for gallbladder cancer, 97% of extrahepatic bile duct cancer, 91% of ampula of Vater cancer, 96% of intrahepatic bile duct cancer, and 94% of hepatocellular carcinoma. Although the OR for gallbladder cancer could not be calculated, the OR for the other sites were 7.01 (95% confidence interval [CI]: 0.79-62.33), 2.21 (0.19-25.52), 10.67 (0.76-150.08), and 1.20 (0.42-3.45), respectively, with an OR of 5.47 (95% CI: 1.17-25.65) observed for the biliary tract cancers combined. ORs above 1 were observed for many of the investigated antigens, although most of these associations were not statistically significant. Seropositivity to H. pylori proteins was associated with an increased risk of biliary tract cancers in ATBC. Further studies are needed to confirm our findings and to determine how H. pylori might influence the risk of biliary tract cancer. © 2014 by the American Association for the Study of Liver Diseases. This article has been contributed to by U.S. Government employees

A comparison of Helicobacter pylori and non-Helicobacter pylori Helicobacter spp. Binding to canine gastric mucosa with defined gastric glycophenotype.

PubMed

Amorim, Irina; Freitas, Daniela P; Magalhães, Ana; Faria, Fátima; Lopes, Célia; Faustino, Augusto M; Smet, Annemieke; Haesebrouck, Freddy; Reis, Celso A; Gärtner, Fátima

2014-08-01

The gastric mucosa of dogs is often colonized by non-Helicobacter pylori helicobacters (NHPH), while H. pylori is the predominant gastric Helicobacter species in humans. The colonization of the human gastric mucosa by H. pylori is highly dependent on the recognition of host glycan receptors. Our goal was to define the canine gastric mucosa glycophenotype and to evaluate the capacity of different gastric Helicobacter species to adhere to the canine gastric mucosa. The glycosylation profile in body and antral compartments of the canine gastric mucosa, with focus on the expression of histo-blood group antigens was evaluated. The in vitro binding capacity of FITC-labeled H. pylori and NHPH to the canine gastric mucosa was assessed in cases representative of the canine glycosylation pattern. The canine gastric mucosa lacks expression of type 1 Lewis antigens and presents a broad expression of type 2 structures and A antigen, both in the surface and glandular epithelium. Regarding the canine antral mucosa, H. heilmannii s.s. presented the highest adhesion score whereas in the body region the SabA-positive H. pylori strain was the strain that adhered more. The canine gastric mucosa showed a glycosylation profile different from the human gastric mucosa suggesting that alternative glycan receptors may be involved in Helicobacter spp. binding. Helicobacter pylori and NHPH strains differ in their ability to adhere to canine gastric mucosa. Among the NHPH, H. heilmannii s.s. presented the highest adhesion capacity in agreement with its reported colonization of the canine stomach. © 2014 John Wiley & Sons Ltd.

Association of seropositivity to Helicobacter species and biliary tract cancer in the ATBC study

PubMed Central

Murphy, Gwen; Michel, Angelika; Taylor, Philip R.; Albanes, Demetrius; Weinstein, Stephanie J.; Virtamo, Jarmo; Parisi, Dominick; Snyder, Kirk; Butt, Julia; McGlynn, Katherine A.; Koshiol, Jill; Pawlita, Michael; Lai, Gabriel Y.; Abnet, Christian C.; Dawsey, Sanford M.; Freedman, Neal D.

2014-01-01

Background Helicobacter have been detected in human bile and hepatobiliary tissue. Despite evidence that Helicobacter species promote gallstone formation and hepatobiliary tumors in laboratory studies, it remains unclear whether Helicobacter species contribute to these cancers in humans. We used a multiplex panel to assess whether seropositivity to 15 Helicobacter pylori (H. pylori) proteins was associated with subsequent incidence of hepatobiliary cancers in the Finnish Alpha-Tocopherol, Beta-Carotene Cancer Prevention (ATBC) Study. Methods We included 64 biliary cancers, 122 liver cancers, and 224 age-matched controls which occurred over the course of 22 years. H. pylori seropositivity was defined as those positive to ≥4 antigens. Odds ratios (OR) and 95% confidence intervals were adjusted for major hepatobiliary cancer risk factors. Results Among the controls, 88% were seropositive to H. pylori at baseline. Among those who subsequently developed hepatobiliary cancer, the prevalence of seropositivity was higher: 100% for gallbladder cancer, 97% of extrahepatic bile duct cancer, 91% of Ampula of vater cancer, 96% of intrahepatic bile duct cancer, and 94% of hepatocellular carcinoma. Although the OR for gallbladder cancer could not be calculated, the OR for the other sites were 7.01 (0.79-62.33), 2.21 (0.19-25.52), 10.67 (0.76-150.08), and 1.20 (0.42-3.45), respectively, with an OR of 5.47 (95%CI: 1.17-25.65) observed for the biliary tract cancers combined. ORs above one were observed for many of the investigated antigens, although most of these associations were not statistically significant. Conclusions Seropositivity to H. pylori proteins was associated with an increased risk of biliary tract cancers in ATBC. Further studies are needed to confirm our findings and to determine how H. pylori might influence risk of biliary tract cancer. PMID:24797247

Gastric Helicobacter species as a cause of feline gastric lymphoma: A viable hypothesis

PubMed Central

Bridgeford, Erin C.; Marini, Robert P.; Feng, Yan; Parry, Nicola M.A.; Rickman, Barry; Fox, James G.

2009-01-01

Gastric Helicobacter spp. are associated with chronic inflammation and neoplastic transformation in humans as well as domestic and laboratory species. The present study examined the association of Helicobacter heilmannii (Hhe) infection in pet cats with feline gastric mucosa associated lymphoid tissue (MALT) lymphoma. Tissues were collected via gastric biopsy or at necropsy from 47 pet cats with clinical signs of gastrointestinal disease, including vomiting and inappetance, and classified as gastritis (14/47), lymphoma (31/37), or normal (2/47). Tissues positive for argyrophilic organisms with Warthin–Starry stain (29/47) were assessed by fluorescent in situ hybridization (FISH) for the presence of Hhe strains 1–4 as well as with a fifth probe that detected Helicobacter salomonis, Helicobacter bizzozeronii, or Helicobacter felis. A significant association of positive Warthin–Starry status with Hhe infection was found in cases of sick cats (22/29; p < 0.05 by Chi-square; χ2 = 7.034). Interestingly, a significant association between Hhe status and a diagnosis of lymphoblastic or lymphocytic lymphoma was observed as well in a subset of 24 Warthin–Starry positive lymphoma cases: of lymphoblastic lymphoma cases, 13/17 were positive for Hhe ( p < 0.05; χ2 = 4.854). Hhe strains 2 and 4 were most commonly found (18/29 and 17/29, respectively) among sick cats, although a higher than expected number of cats was also positive for Hhe1, which initial reports have described as rare in cats and common in humans. The association found between a positive Hhe status with the presence of feline gastric lymphoma, especially lymphoblastic lymphoma, argues for the need to conduct prospective studies to better identify the frequency and strain distribution of Hhe infection in both healthy and clinically ill cats, particularly those cats with gastric lymphoma. PMID:18387674

Minimal standards for describing new species belonging to the families Campylobacteraceae and Helicobacteraceae: Campylobacter, Arcobacter, Helicobacter and Wolinella spp.

PubMed Central

On, Stephen L. W.; Miller, William G.; Houf, Kurt; Fox, James G.; Vandamme, Peter

2017-01-01

Ongoing changes in taxonomic methods, and in the rapid development of the taxonomic structure of species assigned to the Epsilonproteobacteria have lead the International Committee of Systematic Bacteriology Subcommittee on the Taxonomy of Campylobacter and Related Bacteria to discuss significant updates to previous minimal standards for describing new species of Campylobacteraceae and Helicobacteraceae. This paper is the result of these discussions and proposes minimum requirements for the description of new species belonging to the families Campylobacteraceae and Helicobacteraceae, thus including species in Campylobacter, Arcobacter, Helicobacter, and Wolinella. The core underlying principle remains the use of appropriate phenotypic and genotypic methods to characterise strains sufficiently so as to effectively and unambiguously determine their taxonomic position in these families, and provide adequate means by which the new taxon can be distinguished from extant species and subspecies. This polyphasic taxonomic approach demands the use of appropriate reference data for comparison to ensure the novelty of proposed new taxa, and the recommended study of at least five strains to enable species diversity to be assessed. Methodological approaches for phenotypic and genotypic (including whole-genome sequence comparisons) characterisation are recommended. PMID:29034857

Helicobacter-negative gastritis: polymerase chain reaction for Helicobacter DNA is a valuable tool to elucidate the diagnosis.

PubMed

Kiss, S; Zsikla, V; Frank, A; Willi, N; Cathomas, G

2016-04-01

Helicobacter-negative gastritis has been increasingly reported. Molecular techniques as the polymerase chain reaction (PCR) may detect bacterial DNA in histologically negative gastritis. To evaluate of Helicobacter PCR in gastric biopsies for the daily diagnostics of Helicobacter-negative gastritis. Over a 5-year period, routine biopsies with chronic gastritis reminiscent of Helicobacter infection, but negative by histology, were tested by using a H. pylori specific PCR. Subsequently, PCR-negative samples were re-evaluated using PCR for other Helicobacter species. Of the 9184 gastric biopsies, 339 (3.7%) with histological-negative gastritis and adequate material were forwarded to PCR analysis for H. pylori and 146 (43.1%) revealed a positive result. In 193 H. pylori DNA-negative biopsies, re-analysis using PCR primers for other Helicobacter species, revealed further 23 (11.9%) positive biopsies, including 4 (2.1%) biopsies with H. heilmannii sensu lato. PCR-positive biopsies showed a higher overall inflammatory score, more lymphoid follicles/aggregates and neutrophils (P < 0.05). No Helicobacter DNA was found in control biopsies of 48 patients with neither primer set (P < 0.0001). In 274 patients with an endoscopic description, detection of H. pylori DNA was associated with ulcers and erosions (P < 0.01). Over all, in 339 histologically-negative gastric biopsies, Helicobacter DNA was detected in 169 (49.9%) samples with at least one primer set. Molecular testing offers a sensitive and specific diagnosis to a selected group of patients, in whom adequate searches for bacteria by conventional histology have resulted in the unsatisfactory diagnosis of H. pylori-negative gastritis. © 2016 John Wiley & Sons Ltd.

Coinfection with Enterohepatic Helicobacter Species Can Ameliorate or Promote Helicobacter pylori-Induced Gastric Pathology in C57BL/6 Mice ▿

PubMed Central

Ge, Zhongming; Feng, Yan; Muthupalani, Sureshkumar; Eurell, Laura Lemke; Taylor, Nancy S.; Whary, Mark T.; Fox, James G.

2011-01-01

To investigate how different enterohepatic Helicobacter species (EHS) influence Helicobacter pylori gastric pathology, C57BL/6 mice were infected with Helicobacter hepaticus or Helicobacter muridarum, followed by H. pylori infection 2 weeks later. Compared to H. pylori-infected mice, mice infected with H. muridarum and H. pylori (HmHp mice) developed significantly lower histopathologic activity index (HAI) scores (P < 0.0001) at 6 and 11 months postinoculation (MPI). However, mice infected with H. hepaticus and H. pylori (HhHp mice) developed more severe gastric pathology at 6 MPI (P = 0.01), with a HAI at 11 MPI (P = 0.8) similar to that of H. pylori-infected mice. H. muridarum-mediated attenuation of gastritis in coinfected mice was associated with significant downregulation of proinflammatory Th1 (interlukin-1beta [Il-1β], gamma interferon [Ifn-γ], and tumor necrosis factor-alpha [Tnf-α]) cytokines at both time points and Th17 (Il-17A) cytokine mRNA levels at 6 MPI in murine stomachs compared to those of H. pylori-infected mice (P < 0.01). Coinfection with H. hepaticus also suppressed H. pylori-induced elevation of gastric Th1 cytokines Ifn-γ and Tnf-α (P < 0.0001) but increased Th17 cytokine mRNA levels (P = 0.028) at 6 MPI. Furthermore, mRNA levels of Il-17A were positively correlated with the severity of helicobacter-induced gastric pathology (HhHp>H. pylori>HmHp) (at 6 MPI, r2 = 0.92, P < 0.0001; at 11 MPI, r2 = 0.82, P < 0.002). Despite disparate effects on gastritis, colonization levels of gastric H. pylori were increased in HhHp mice (at 6 MPI) and HmHp mice (at both time points) compared to those in mono-H. pylori-infected mice. These data suggest that despite consistent downregulation of Th1 responses, EHS coinfection either attenuated or promoted the severity of H. pylori-induced gastric pathology in C57BL/6 mice. This modulation was related to the variable effects of EHS on gastric interleukin 17 (IL-17) responses to H. pylori infection. PMID

Phylogeographic diversity and mosaicism of the Helicobacter pylori tfs integrative and conjugative elements.

PubMed

Delahay, Robin M; Croxall, Nicola J; Stephens, Amberley D

2018-01-01

The genome of the gastric pathogen Helicobacter pylori is characterised by considerable variation of both gene sequence and content, much of which is contained within three large genomic islands comprising the cag pathogenicity island ( cag PAI) and two mobile integrative and conjugative elements (ICEs) termed tfs3 and tfs4 . All three islands are implicated as virulence factors, although whereas the cag PAI is well characterised, understanding of how the tfs elements influence H. pylori interactions with different human hosts is significantly confounded by limited definition of their distribution, diversity and structural representation in the global H. pylori population. To gain a global perspective of tfs ICE population dynamics we established a bioinformatics workflow to extract and precisely define the full tfs pan-gene content contained within a global collection of 221 draft and complete H. pylori genome sequences. Complete (ca. 35-55kbp) and remnant tfs ICE clusters were reconstructed from a dataset comprising > 12,000 genes, from which orthologous gene complements and distinct alleles descriptive of different tfs ICE types were defined and classified in comparative analyses. The genetic variation within defined ICE modular segments was subsequently used to provide a complete description of tfs ICE diversity and a comprehensive assessment of their phylogeographic context. Our further examination of the apparent ICE modular types identified an ancient and complex history of ICE residence, mobility and interaction within particular H. pylori phylogeographic lineages and further, provided evidence of both contemporary inter-lineage and inter-species ICE transfer and displacement. Our collective results establish a clear view of tfs ICE diversity and phylogeographic representation in the global H. pylori population, and provide a robust contextual framework for elucidating the functional role of the tfs ICEs particularly as it relates to the risk of gastric

Lethal photosensitization of Helicobacter species

NASA Astrophysics Data System (ADS)

Millson, Charles E.; Wilson, Michael; MacRobert, Alexander J.; Thurrell, Wendy; Mlkvy, Peter; Davies, Claire; Bown, Stephen G.

1995-01-01

Helicobacter pylori (H. pylori) is associated with a large number of gastroduodenal disorders. Clearance of the bacteria has been shown to benefit patients with duodenal ulcers, gastric ulcers, and certain rare types of gastric tumors. Broad-spectrum antibiotics are the mainstay of current treatment strategies but side-effects, poor compliance, and drug resistance limit their usefulness. We sensitized H. pylori with toluidine blue, haematoporphyrin derivative, aluminum disulphonated phthalocyanine, methylene blue or protoporphyrin IX prior to exposure to low-power laser light from either a gallium aluminum arsenide laser or a helium neon gas laser. All 5 sensitizers caused reductions of greater than 1000-fold in the number of viable bacteria. Light alone had no effect and only HpD caused a significant decrease in bacterial numbers without laser light. Next, we sensitized H. mustelae on explanted ferret gastric mucosa (ex vivo) with the same sensitizers and exposed them to light from a copper vapor pumped dye laser tuned appropriately. MB caused significant reductions in bacterial counts. Successful lethal photosensitization of Helicobacter pylori both in vitro and ex vivo raises the possibility of a local method for eradicating the bacteria, especially as the bacteria are only found in those parts of the upper gastrointestinal tract that are accessible to the endoscope.

Novel gastric helicobacters and oral campylobacters are present in captive and wild cetaceans

PubMed Central

Goldman, Cinthia G.; Matteo, Mario J.; Loureiro, Julio D.; Almuzara, Marisa; Barberis, Claudia; Vay, Carlos; Catalano, Mariana; Heredia, Sergio Rodríguez; Mantero, Paula; Boccio, Jose R.; Zubillaga, Marcela B.; Cremaschi, Graciela A.; Solnick, Jay V.; Perez-Perez, Guillermo I.; Blaser, Martin J.

2011-01-01

The mammalian gastric and oral mucosa may be colonized by mixed Helicobacter and Campylobacter species, respectively, in individual animals. To better characterize the presence and distribution of Helicobacter and Campylobacter among marine mammals, we used PCR and 16S rDNA sequence analysis to examine gastric and oral samples from ten dolphins (Tursiops gephyreus), one killer whale (Orcinus orca), one false killer whale (Pseudorca crassidens), and three wild La Plata river dolphins (Pontoporia blainvillei). Helicobacter spp. DNA was widely distributed in gastric and oral samples from both captive and wild cetaceans. Phylogenetic analysis demonstrated two Helicobacter sequence clusters, one closely related to H. cetorum, a species isolated from dolphins and whales in North America. The second related cluster was to sequences obtained from dolphins in Australia and to gastric non-Helicobacter pylori helicobacters, and may represent a novel taxonomic group. Dental plaque sequences from four dolphins formed a third cluster within the Campylobacter genus that likely represents a novel species isolated from marine mammals. Identification of identical Helicobacter spp. DNA sequences from dental plaque, saliva and gastric fluids from the same hosts, suggests that the oral cavity may be involved in transmission. These results demonstrate that Helicobacter and Campylobacter species are commonly distributed in marine mammals, and identify taxonomic clusters that may represent novel species. PMID:21592686

Phylogenetically diverse macrophyte community promotes species diversity of mobile epi-benthic invertebrates

NASA Astrophysics Data System (ADS)

Nakamoto, Kenta; Hayakawa, Jun; Kawamura, Tomohiko; Kodama, Masafumi; Yamada, Hideaki; Kitagawa, Takashi; Watanabe, Yoshiro

2018-07-01

Various aspects of plant diversity such as species diversity and phylogenetic diversity enhance the species diversity of associated animals in terrestrial systems. In marine systems, however, the effects of macrophyte diversity on the species diversity of associated animals have received little attention. Here, we sampled in a subtropical seagrass-seaweed mixed bed to elucidate the effect of the macrophyte phylogenetic diversity based on the taxonomic relatedness as well as the macrophyte species diversity on species diversity of mobile epi-benthic invertebrates. Using regression analyses for each macrophyte parameter as well as multiple regression analyses, we found that the macrophyte phylogenetic diversity (taxonomic diversity index: Delta) positively influenced the invertebrate species richness and diversity index (H‧). Although the macrophyte species richness and H‧ also positively influenced the invertebrate species richness, the best fit model for invertebrate species richness did not include them, suggesting that the macrophyte species diversity indirectly influenced invertebrate species diversity. Possible explanations of the effects of macrophyte Delta on the invertebrate species diversity were the niche complementarity effect and the selection effect. This is the first study which demonstrates that macrophyte phylogenetic diversity has a strong effect on the species diversity of mobile epi-benthic invertebrates.

Helicobacter Infection Significantly Alters Pregnancy Success in Laboratory Mice.

PubMed

Bracken, Tara C; Cooper, Caitlin A; Ali, Zil; Truong, Ha; Moore, Julie M

2017-05-01

Helicobacter spp. are gram-negative, helically shaped bacteria that cause gastric and enterohepatic infections in mammalian species. Although Helicobacter infection frequently is implicated to interfere with reproductive success, few experimental data support these claims. We therefore retrospectively investigated the effect of Helicobacter infection on murine pregnancy outcome after the identification of endemic Helicobacter infection in an animal research facility. Multiplex conventional PCR analysis was used to characterize Helicobacter infection status in one inbred and 2 transgenic strains of mice in 2 self-contained rooms assigned to the same investigator. Outcomes of timed-mating experiments were compared among Helicobacter spp.-infected and uninfected mice of the same strain; Helicobacter infection was eradicated from the colony through fostering with uninfected dams. Although Helicobacter infection affected fecundity in only one strain of transgenic mouse, the total number of embryos per gravid uterus was significantly reduced in C57BL/6J mice that were infected with a single Helicobacter species, H. typhlonius. Helicobacter infection was also associated with a significant increase in the number of resorbing embryos per uterus and significant decreases in pregnancy-associated weight gain relative to uninfected mice in C57BL6/J mice and one transgenic strain. Helicobacter spp.-infected mice of all tested strains exhibited higher frequency of intrauterine hemorrhaging relative to uninfected mice. These results indicate that naturally-acquired Helicobacter infection not only reduces the productivity of a research animal breeding colony, but also negatively impacts embryo health. Despite these deleterious effects, these data suggest that colonies can be rederived to be Helicobacter-free by Cesarean section and fostering with uninfected dams. This paper provides the first evidence that H. typhlonius infection is sufficient to interfere with reproductive success

Sequence Divergence and Conservation in Genomes of Helicobacter cetorum Strains from a Dolphin and a Whale

PubMed Central

Kersulyte, Dangeruta; Rossi, Mirko; Berg, Douglas E.

2013-01-01

Background and Objectives Strains of Helicobacter cetorum have been cultured from several marine mammals and have been found to be closely related in 16 S rDNA sequence to the human gastric pathogen H. pylori, but their genomes were not characterized further. Methods The genomes of H. cetorum strains from a dolphin and a whale were sequenced completely using 454 technology and PCR and capillary sequencing. Results These genomes are 1.8 and 1.95 mb in size, some 7–26% larger than H. pylori genomes, and differ markedly from one another in gene content, and sequences and arrangements of shared genes. However, each strain is more related overall to H. pylori and its descendant H. acinonychis than to other known species. These H. cetorum strains lack cag pathogenicity islands, but contain novel alleles of the virulence-associated vacuolating cytotoxin (vacA) gene. Of particular note are (i) an extra triplet of vacA genes with ≤50% protein-level identity to each other in the 5′ two-thirds of the gene needed for host factor interaction; (ii) divergent sets of outer membrane protein genes; (iii) several metabolic genes distinct from those of H. pylori; (iv) genes for an iron-cofactored urease related to those of Helicobacter species from terrestrial carnivores, in addition to genes for a nickel co-factored urease; and (v) members of the slr multigene family, some of which modulate host responses to infection and improve Helicobacter growth with mammalian cells. Conclusions Our genome sequence data provide a glimpse into the novelty and great genetic diversity of marine helicobacters. These data should aid further analyses of microbial genome diversity and evolution and infection and disease mechanisms in vast and often fragile ocean ecosystems. PMID:24358262

Helicobacter pylori Diversity and Gastric Cancer Risk

PubMed Central

2016-01-01

ABSTRACT Gastric cancer is a leading cause of cancer-related death worldwide. Helicobacter pylori infection is the strongest known risk factor for this malignancy. An important goal is to identify H. pylori-infected persons at high risk for gastric cancer, so that these individuals can be targeted for therapeutic intervention. H. pylori exhibits a high level of intraspecies genetic diversity, and over the past two decades, many studies have endeavored to identify strain-specific features of H. pylori that are linked to development of gastric cancer. One of the most prominent differences among H. pylori strains is the presence or absence of a 40-kb chromosomal region known as the cag pathogenicity island (PAI). Current evidence suggests that the risk of gastric cancer is very low among persons harboring H. pylori strains that lack the cag PAI. Among persons harboring strains that contain the cag PAI, the risk of gastric cancer is shaped by a complex interplay among multiple strain-specific bacterial factors as well as host factors. This review discusses the strain-specific properties of H. pylori that correlate with increased gastric cancer risk, focusing in particular on secreted proteins and surface-exposed proteins, and describes evidence from cell culture and animal models linking these factors to gastric cancer pathogenesis. Strain-specific features of H. pylori that may account for geographic variation in gastric cancer incidence are also discussed. PMID:26814181

OVERVIEW: DISINFECTION OF HELICOBACTER PYLORI AND AEROMONAS SPECIES

EPA Science Inventory

Helicobacter pylori and Aeromonas hydrophila are contaminants listed on the USEPA's 1998 Contaminant Candidate List (CCL).The sensitivity of H. pylori to chlorine and of Aeromonas spp. to inactivation by free chlorine, chloramine and ultraviolet (UV) was examined. Selective and...

Multiplex PCR Assay for Differentiation of Helicobacter felis, H. bizzozeronii, and H. salomonis

PubMed Central

Baele, M.; Van den Bulck, K.; Decostere, A.; Vandamme, P.; Hänninen, M.-L.; Ducatelle, R.; Haesebrouck, F.

2004-01-01

Helicobacter felis, Helicobacter bizzozeronii, and Helicobacter salomonis are frequently found in the gastric mucous membrane of dogs and cats. These large spiral organisms are phylogenetically highly related to each other. Their fastidious nature makes it difficult to cultivate them in vitro, hampering traditional identification methods. We describe here a multiplex PCR test based on the tRNA intergenic spacers and on the urease gene, combined with capillary electrophoresis, that allows discrimination of these three species. In combination with previously described 16S ribosomal DNA-based primers specific for the nonculturable “Candidatus Helicobacter suis,” our procedure was shown to be very useful in determining the species identity of “Helicobacter heilmannii”-like organisms observed in human stomachs and will facilitate research concerning their possible zoonotic importance. PMID:15004062

Colonization of the Cecal Mucosa by Helicobacter hepaticus Impacts the Diversity of the Indigenous Microbiota

PubMed Central

Kuehl, Carole J.; Wood, Heather D.; Marsh, Terence L.; Schmidt, Thomas M.; Young, Vincent B.

2005-01-01

Establishment of mucosal and/or luminal colonization is the first step in the pathogenesis of many gastrointestinal bacterial pathogens. The pathogen must be able to establish itself in the face of competition from the complex microbial community that is already in place. We used culture-independent methods to monitor the colonization of the cecal mucosa of Helicobacter-free mice following experimental infection with the pathogen Helicobacter hepaticus. Two days after infection, H. hepaticus comprised a minor component of the mucosa-associated microbiota, but within 14 days, it became the dominant member of the community. Colonization of the mucosa by H. hepaticus was associated with a decrease in the overall diversity of the microbial community, in large part due to changes in evenness resulting from the relative dominance of H. hepaticus as a member of the community. Our results demonstrate that invasion of the complex gastrointestinal microbial community by a pathogenic microorganism causes reproducible and significant disturbances in the community structure. The use of non-culture-based methods to monitor these changes should lead to a greater understanding of the ecological principles that govern pathogen invasion and may lead to novel methods for the prevention and control of gastrointestinal pathogens. PMID:16177375

A Global Overview of the Genetic and Functional Diversity in the Helicobacter pylori cag Pathogenicity Island

PubMed Central

Moodley, Yoshan; Uhr, Markus; Stamer, Christiana; Vauterin, Marc; Suerbaum, Sebastian; Achtman, Mark

2010-01-01

The Helicobacter pylori cag pathogenicity island (cagPAI) encodes a type IV secretion system. Humans infected with cagPAI–carrying H. pylori are at increased risk for sequelae such as gastric cancer. Housekeeping genes in H. pylori show considerable genetic diversity; but the diversity of virulence factors such as the cagPAI, which transports the bacterial oncogene CagA into host cells, has not been systematically investigated. Here we compared the complete cagPAI sequences for 38 representative isolates from all known H. pylori biogeographic populations. Their gene content and gene order were highly conserved. The phylogeny of most cagPAI genes was similar to that of housekeeping genes, indicating that the cagPAI was probably acquired only once by H. pylori, and its genetic diversity reflects the isolation by distance that has shaped this bacterial species since modern humans migrated out of Africa. Most isolates induced IL-8 release in gastric epithelial cells, indicating that the function of the Cag secretion system has been conserved despite some genetic rearrangements. More than one third of cagPAI genes, in particular those encoding cell-surface exposed proteins, showed signatures of diversifying (Darwinian) selection at more than 5% of codons. Several unknown gene products predicted to be under Darwinian selection are also likely to be secreted proteins (e.g. HP0522, HP0535). One of these, HP0535, is predicted to code for either a new secreted candidate effector protein or a protein which interacts with CagA because it contains two genetic lineages, similar to cagA. Our study provides a resource that can guide future research on the biological roles and host interactions of cagPAI proteins, including several whose function is still unknown. PMID:20808891

A global overview of the genetic and functional diversity in the Helicobacter pylori cag pathogenicity island.

PubMed

Olbermann, Patrick; Josenhans, Christine; Moodley, Yoshan; Uhr, Markus; Stamer, Christiana; Vauterin, Marc; Suerbaum, Sebastian; Achtman, Mark; Linz, Bodo

2010-08-19

The Helicobacter pylori cag pathogenicity island (cagPAI) encodes a type IV secretion system. Humans infected with cagPAI-carrying H. pylori are at increased risk for sequelae such as gastric cancer. Housekeeping genes in H. pylori show considerable genetic diversity; but the diversity of virulence factors such as the cagPAI, which transports the bacterial oncogene CagA into host cells, has not been systematically investigated. Here we compared the complete cagPAI sequences for 38 representative isolates from all known H. pylori biogeographic populations. Their gene content and gene order were highly conserved. The phylogeny of most cagPAI genes was similar to that of housekeeping genes, indicating that the cagPAI was probably acquired only once by H. pylori, and its genetic diversity reflects the isolation by distance that has shaped this bacterial species since modern humans migrated out of Africa. Most isolates induced IL-8 release in gastric epithelial cells, indicating that the function of the Cag secretion system has been conserved despite some genetic rearrangements. More than one third of cagPAI genes, in particular those encoding cell-surface exposed proteins, showed signatures of diversifying (Darwinian) selection at more than 5% of codons. Several unknown gene products predicted to be under Darwinian selection are also likely to be secreted proteins (e.g. HP0522, HP0535). One of these, HP0535, is predicted to code for either a new secreted candidate effector protein or a protein which interacts with CagA because it contains two genetic lineages, similar to cagA. Our study provides a resource that can guide future research on the biological roles and host interactions of cagPAI proteins, including several whose function is still unknown.

Intraspecific genetic diversity and composition modify species-level diversity-productivity relationships.

PubMed

Schöb, Christian; Kerle, Sarah; Karley, Alison J; Morcillo, Luna; Pakeman, Robin J; Newton, Adrian C; Brooker, Rob W

2015-01-01

Biodiversity regulates ecosystem functions such as productivity, and experimental studies of species mixtures have revealed selection and complementarity effects driving these responses. However, the impacts of intraspecific genotypic diversity in these studies are unknown, despite it forming a substantial part of the biodiversity. In a glasshouse experiment we constructed plant communities with different levels of barley (Hordeum vulgare) genotype and weed species diversity and assessed their relative biodiversity effects through additive partitioning into selection and complementarity effects. Barley genotype diversity had weak positive effects on aboveground biomass through complementarity effects, whereas weed species diversity increased biomass predominantly through selection effects. When combined, increasing genotype diversity of barley tended to dilute the selection effect of weeds. We interpret these different effects of barley genotype and weed species diversity as the consequence of small vs large trait variation associated with intraspecific barley diversity and interspecific weed diversity, respectively. The different effects of intra- vs interspecific diversity highlight the underestimated and overlooked role of genetic diversity for ecosystem functioning. © 2014 The Authors New Phytologist © 2014 New Phytologist Trust.

Gastric Helicobacters in Domestic Animals and Nonhuman Primates and Their Significance for Human Health

PubMed Central

Haesebrouck, Freddy; Pasmans, Frank; Flahou, Bram; Chiers, Koen; Baele, Margo; Meyns, Tom; Decostere, Annemie; Ducatelle, Richard

2009-01-01

Summary: Helicobacters other than Helicobacter pylori have been associated with gastritis, gastric ulcers, and gastric mucosa-associated lymphoid tissue lymphoma in humans. These very fastidious microorganisms with a typical large spiral-shaped morphology were provisionally designated “H. heilmannii,” but in fact they comprise at least five different Helicobacter species, all of which are known to colonize the gastric mucosa of animals. H. suis, which has been isolated from the stomachs of pigs, is the most prevalent gastric non-H. pylori Helicobacter species in humans. Other gastric non-H. pylori helicobacters colonizing the human stomach are H. felis, H. salomonis, H. bizzozeronii, and the still-uncultivable “Candidatus Helicobacter heilmannii.” These microorganisms are often detected in the stomachs of dogs and cats. “Candidatus Helicobacter bovis” is highly prevalent in the abomasums of cattle but has only occasionally been detected in the stomachs of humans. There are clear indications that gastric non-H. pylori Helicobacter infections in humans originate from animals, and it is likely that transmission to humans occurs through direct contact. Little is known about the virulence factors of these microorganisms. The recent successes with in vitro isolation of non-H. pylori helicobacters from domestic animals open new perspectives for studying these microorganisms and their interactions with the host. PMID:19366912

Simulated tri-trophic networks reveal complex relationships between species diversity and interaction diversity

PubMed Central

Lumpkin, Will; Hurtado, Paul J.; Dyer, Lee A.

2018-01-01

Most of earth’s biodiversity is comprised of interactions among species, yet it is unclear what causes variation in interaction diversity across space and time. We define interaction diversity as the richness and relative abundance of interactions linking species together at scales from localized, measurable webs to entire ecosystems. Large-scale patterns suggest that two basic components of interaction diversity differ substantially and predictably between different ecosystems: overall taxonomic diversity and host specificity of consumers. Understanding how these factors influence interaction diversity, and quantifying the causes and effects of variation in interaction diversity are important goals for community ecology. While previous studies have examined the effects of sampling bias and consumer specialization on determining patterns of ecological networks, these studies were restricted to two trophic levels and did not incorporate realistic variation in species diversity and consumer diet breadth. Here, we developed a food web model to generate tri-trophic ecological networks, and evaluated specific hypotheses about how the diversity of trophic interactions and species diversity are related under different scenarios of species richness, taxonomic abundance, and consumer diet breadth. We investigated the accumulation of species and interactions and found that interactions accumulate more quickly; thus, the accumulation of novel interactions may require less sampling effort than sampling species in order to get reliable estimates of either type of diversity. Mean consumer diet breadth influenced the correlation between species and interaction diversity significantly more than variation in both species richness and taxonomic abundance. However, this effect of diet breadth on interaction diversity is conditional on the number of observed interactions included in the models. The results presented here will help develop realistic predictions of the relationships

Simulated tri-trophic networks reveal complex relationships between species diversity and interaction diversity.

PubMed

Pardikes, Nicholas A; Lumpkin, Will; Hurtado, Paul J; Dyer, Lee A

2018-01-01

Most of earth's biodiversity is comprised of interactions among species, yet it is unclear what causes variation in interaction diversity across space and time. We define interaction diversity as the richness and relative abundance of interactions linking species together at scales from localized, measurable webs to entire ecosystems. Large-scale patterns suggest that two basic components of interaction diversity differ substantially and predictably between different ecosystems: overall taxonomic diversity and host specificity of consumers. Understanding how these factors influence interaction diversity, and quantifying the causes and effects of variation in interaction diversity are important goals for community ecology. While previous studies have examined the effects of sampling bias and consumer specialization on determining patterns of ecological networks, these studies were restricted to two trophic levels and did not incorporate realistic variation in species diversity and consumer diet breadth. Here, we developed a food web model to generate tri-trophic ecological networks, and evaluated specific hypotheses about how the diversity of trophic interactions and species diversity are related under different scenarios of species richness, taxonomic abundance, and consumer diet breadth. We investigated the accumulation of species and interactions and found that interactions accumulate more quickly; thus, the accumulation of novel interactions may require less sampling effort than sampling species in order to get reliable estimates of either type of diversity. Mean consumer diet breadth influenced the correlation between species and interaction diversity significantly more than variation in both species richness and taxonomic abundance. However, this effect of diet breadth on interaction diversity is conditional on the number of observed interactions included in the models. The results presented here will help develop realistic predictions of the relationships

Genetic diversity of the HpyC1I restriction modification system in Helicobacter pylori.

PubMed

Lehours, Philippe; Dupouy, Sandrine; Chaineux, Julien; Ruskoné-Fourmestraux, Agnès; Delchier, Jean-Charles; Morgner, Andrea; Mégraud, Francis; Ménard, Armelle

2007-04-01

Helicobacter pylori is unique because of the unusually high number and diversity of its restriction modification (R-M) systems. HpyC1I R-M was recently characterized and contains an endonuclease which is an isoschizomer of the endonuclease BccI. This R-M is involved in adherence to gastric epithelial cells, a crucial step in bacterial pathogenesis. This observation illustrates the fact that R-M systems have other putative biological functions in addition to protecting the bacterial genome from external DNA. The genomic diversity of HpyC1I R-M was evaluated more precisely on a large collection of H. pylori strains by PCR, susceptibility to BccI digestion and sequencing. The results obtained support the mechanism of gain and loss of this R-M system in the H. pylori genome, and suggest that it is an ancestral system which gradually disappears during H. pylori evolution, following successive steps: (1) inactivation of the endonuclease gene, followed or accompanied by: (2) inactivation of the methyltransferase genes, and then: (3) definitive loss, leaving only short endonuclease remnant sequences.

Enterohepatic helicobacter in ulcerative colitis: potential pathogenic entities?

PubMed

Thomson, John M; Hansen, Richard; Berry, Susan H; Hope, Mairi E; Murray, Graeme I; Mukhopadhya, Indrani; McLean, Mairi H; Shen, Zeli; Fox, James G; El-Omar, Emad; Hold, Georgina L

2011-02-23

Changes in bacterial populations termed "dysbiosis" are thought central to ulcerative colitis (UC) pathogenesis. In particular, the possibility that novel Helicobacter organisms play a role in human UC has been debated but not comprehensively investigated. The aim of this study was to develop a molecular approach to investigate the presence of Helicobacter organisms in adults with and without UC. A dual molecular approach to detect Helicobacter was developed. Oligonucleotide probes against the genus Helicobacter were designed and optimised alongside a validation of published H. pylori probes. A comprehensive evaluation of Helicobacter genus and H. pylori PCR primers was also undertaken. The combined approach was then assessed in a range of gastrointestinal samples prior to assessment of a UC cohort. Archival colonic samples were available from 106 individuals for FISH analysis (57 with UC and 49 non-IBD controls). A further 118 individuals were collected prospectively for dual FISH and PCR analysis (86 UC and 32 non-IBD controls). An additional 27 non-IBD controls were available for PCR analysis. All Helicobacter PCR-positive samples were sequenced. The association between Helicobacter and each study group was statistically analysed using the Pearson Chi Squared 2 tailed test. Helicobacter genus PCR positivity was significantly higher in UC than controls (32 of 77 versus 11 of 59, p = 0.004). Sequence analysis indicated enterohepatic Helicobacter species prevalence was significantly higher in the UC group compared to the control group (30 of 77 versus 2 of 59, p<0.0001). PCR and FISH results were concordant in 74 (67.9%) of subjects. The majority of discordant results were attributable to a higher positivity rate with FISH than PCR. Helicobacter organisms warrant consideration as potential pathogenic entities in UC. Isolation of these organisms from colonic tissue is needed to enable interrogation of pathogenicity against established criteria.

Helicobacter spp. from captive bottlenose dolphins (Tursiops spp.) and polar bears (Ursus maritimus).

PubMed

Oxley, Andrew P A; Argo, Jeffrey A; McKay, David B

2005-11-01

The gastric fluid of six bottlenose dolphins and the faeces of four polar bears from the same oceanarium were examined for the presence of Helicobacter. As detected by PCR, all dolphins and 8/12 samples collected from polar bears were positive for Helicobacter. Novel sequence types were identified in samples collected from these animals of which several were unique to either the dolphins or the polar bears. At least one sequence type was, however, detected in both animal taxa. In addition, a sequence type from a dolphin shared a 98.2-100% identity to sequences from other Helicobacter species from harp seals, sea otters and sea lions. This study reports on the occurrence of novel Helicobacter sequence types in polar bears and dolphins and demonstrates the broad-host range of some species within these animals.

Helicobacter hepaticus induces an inflammatory response in primary human hepatocytes.

PubMed

Kleine, Moritz; Worbs, Tim; Schrem, Harald; Vondran, Florian W R; Kaltenborn, Alexander; Klempnauer, Jürgen; Förster, Reinhold; Josenhans, Christine; Suerbaum, Sebastian; Bektas, Hüseyin

2014-01-01

Helicobacter hepaticus can lead to chronic hepatitis and hepatocellular carcinoma in certain strains of mice. Until now the pathogenic role of Helicobacter species on human liver tissue is still not clarified though Helicobacter species identification in human liver cancer was successful in case controlled studies. Therefore we established an in vitro model to investigate the interaction of primary human hepatocytes (PHH) with Helicobacter hepaticus. Successful co-culturing of PHH with Helicobacter hepaticus was confirmed by visualization of motile bacteria by two-photon-microscopy. Isolated human monocytes were stimulated with PHH conditioned media. Changes in mRNA expression of acute phase cytokines and proteins in PHH and stimulated monocytes were determined by Real-time PCR. Furthermore, cytokines and proteins were analyzed in PHH culture supernatants by ELISA. Co-cultivation with Helicobacter hepaticus induced mRNA expression of Interleukin-1 beta (IL-1β), Tumor necrosis factor-alpha, Interleukin-8 (IL-8) and Monocyte chemotactic protein-1 (MCP-1) in PHH (p<0.05) resulting in a corresponding increase of IL-8 and MCP-1 concentrations in PHH supernatants (p<0.05). IL-8 and IL-1β mRNA expression was induced in monocytes stimulated with Helicobacter hepaticus infected PHH conditioned media (p<0.05). An increase of Cyclooxygenase-2 mRNA expression was observed, with a concomitant increase of prostaglandin E2 concentration in PHH supernatants at 24 and 48 h (p<0.05). In contrast, at day 7 of co-culture, no persistent elevation of cytokine mRNA could be detected. High expression of intercellular adhesion molecule-1 on PHH cell membranes after co-culture was shown by two-photon-microscopy and confirmed by flow-cytometry. Finally, expression of Cytochrome P450 3A4 and albumin mRNA were downregulated, indicating an impairment of hepatocyte synthesis function by Helicobacter hepaticus presence. This is the first in vitro model demonstrating a pathogenic effect of a

Genetic diversity and species diversity of stream fishes covary across a land-use gradient.

PubMed

Blum, Michael J; Bagley, Mark J; Walters, David M; Jackson, Suzanne A; Daniel, F Bernard; Chaloud, Deborah J; Cade, Brian S

2012-01-01

Genetic diversity and species diversity are expected to covary according to area and isolation, but may not always covary with environmental heterogeneity. In this study, we examined how patterns of genetic and species diversity in stream fishes correspond to local and regional environmental conditions. To do so, we compared population size, genetic diversity and divergence in central stonerollers (Campostoma anomalum) to measures of species diversity and turnover in stream fish assemblages among similarly sized watersheds across an agriculture-forest land-use gradient in the Little Miami River basin (Ohio, USA). Significant correlations were found in many, but not all, pair-wise comparisons. Allelic richness and species richness were strongly correlated, for example, but diversity measures based on allele frequencies and assemblage structure were not. In-stream conditions related to agricultural land use were identified as significant predictors of genetic diversity and species diversity. Comparisons to population size indicate, however, that genetic diversity and species diversity are not necessarily independent and that variation also corresponds to watershed location and glaciation history in the drainage basin. Our findings demonstrate that genetic diversity and species diversity can covary in stream fish assemblages, and illustrate the potential importance of scaling observations to capture responses to hierarchical environmental variation. More comparisons according to life history variation could further improve understanding of conditions that give rise to parallel variation in genetic diversity and species diversity, which in turn could improve diagnosis of anthropogenic influences on aquatic ecosystems.

Genetic diversity and species diversity of stream fishes covary across a land-use gradient

USGS Publications Warehouse

Blum, M.J.; Bagley, M.J.; Walters, D.M.; Jackson, S.A.; Daniel, F.B.; Chaloud, D.J.; Cade, B.S.

2012-01-01

Genetic diversity and species diversity are expected to covary according to area and isolation, but may not always covary with environmental heterogeneity. In this study, we examined how patterns of genetic and species diversity in stream fishes correspond to local and regional environmental conditions. To do so, we compared population size, genetic diversity and divergence in central stonerollers (Campostoma anomalum) to measures of species diversity and turnover in stream fish assemblages among similarly sized watersheds across an agriculture-forest land-use gradient in the Little Miami River basin (Ohio, USA). Significant correlations were found in many, but not all, pair-wise comparisons. Allelic richness and species richness were strongly correlated, for example, but diversity measures based on allele frequencies and assemblage structure were not. In-stream conditions related to agricultural land use were identified as significant predictors of genetic diversity and species diversity. Comparisons to population size indicate, however, that genetic diversity and species diversity are not necessarily independent and that variation also corresponds to watershed location and glaciation history in the drainage basin. Our findings demonstrate that genetic diversity and species diversity can covary in stream fish assemblages, and illustrate the potential importance of scaling observations to capture responses to hierarchical environmental variation. More comparisons according to life history variation could further improve understanding of conditions that give rise to parallel variation in genetic diversity and species diversity, which in turn could improve diagnosis of anthropogenic influences on aquatic ecosystems. ?? 2011 Springer-Verlag.

Identification of Helicobacter and Wolinella spp. in Oral Cavity of Toy Breed Dogs With Periodontal Disease.

PubMed

Nowroozilarki, Negar; Jamshidi, Shahram; Zahraei Salehi, Taghi; Kolahian, Saeed

2017-09-01

Periodontal diseases are the most common oral cavity infectious diseases in adult dogs. We aimed in this study to identify Helicobacter and Wolinella spp. in saliva and dental plaque of dogs with periodontitis. Sixty-two small-breed pet dogs, aged more than 6 years from both sexes, were categorized into healthy and periodontitis groups. Samples from saliva and dental plaques were collected, and Helicobacter and Wolinella were identified on genus and species levels using polymerase chain reaction. Our results showed significant increase in infection rate of Wolinella spp. in periodontitis compared with healthy dogs (P = .002). Furthermore, infection rate of Helicobacter genus was significantly higher in periodontitis compared with healthy dogs (P = .007). Infection with Wolinella spp. showed higher rate than Helicobacter spp. in dogs with periodontitis. According to species-specific polymerase chain reaction results, Helicobacter felis (9.76%) was the main Helicobacter spp. in dogs with periodontitis compared with healthy dogs (P < .001). Oral cavity of pet dogs with periodontitis could be considered as an important source of Wolinella and Helicobacter spp. infections. Copyright © 2017 Elsevier Inc. All rights reserved.

Change is good: variations in common biological mechanisms in the epsilonproteobacterial genera Campylobacter and Helicobacter.

PubMed

Gilbreath, Jeremy J; Cody, William L; Merrell, D Scott; Hendrixson, David R

2011-03-01

Microbial evolution and subsequent species diversification enable bacterial organisms to perform common biological processes by a variety of means. The epsilonproteobacteria are a diverse class of prokaryotes that thrive in diverse habitats. Many of these environmental niches are labeled as extreme, whereas other niches include various sites within human, animal, and insect hosts. Some epsilonproteobacteria, such as Campylobacter jejuni and Helicobacter pylori, are common pathogens of humans that inhabit specific regions of the gastrointestinal tract. As such, the biological processes of pathogenic Campylobacter and Helicobacter spp. are often modeled after those of common enteric pathogens such as Salmonella spp. and Escherichia coli. While many exquisite biological mechanisms involving biochemical processes, genetic regulatory pathways, and pathogenesis of disease have been elucidated from studies of Salmonella spp. and E. coli, these paradigms often do not apply to the same processes in the epsilonproteobacteria. Instead, these bacteria often display extensive variation in common biological mechanisms relative to those of other prototypical bacteria. In this review, five biological processes of commonly studied model bacterial species are compared to those of the epsilonproteobacteria C. jejuni and H. pylori. Distinct differences in the processes of flagellar biosynthesis, DNA uptake and recombination, iron homeostasis, interaction with epithelial cells, and protein glycosylation are highlighted. Collectively, these studies support a broader view of the vast repertoire of biological mechanisms employed by bacteria and suggest that future studies of the epsilonproteobacteria will continue to provide novel and interesting information regarding prokaryotic cellular biology.

Change Is Good: Variations in Common Biological Mechanisms in the Epsilonproteobacterial Genera Campylobacter and Helicobacter

PubMed Central

Gilbreath, Jeremy J.; Cody, William L.; Merrell, D. Scott; Hendrixson, David R.

2011-01-01

Summary: Microbial evolution and subsequent species diversification enable bacterial organisms to perform common biological processes by a variety of means. The epsilonproteobacteria are a diverse class of prokaryotes that thrive in diverse habitats. Many of these environmental niches are labeled as extreme, whereas other niches include various sites within human, animal, and insect hosts. Some epsilonproteobacteria, such as Campylobacter jejuni and Helicobacter pylori, are common pathogens of humans that inhabit specific regions of the gastrointestinal tract. As such, the biological processes of pathogenic Campylobacter and Helicobacter spp. are often modeled after those of common enteric pathogens such as Salmonella spp. and Escherichia coli. While many exquisite biological mechanisms involving biochemical processes, genetic regulatory pathways, and pathogenesis of disease have been elucidated from studies of Salmonella spp. and E. coli, these paradigms often do not apply to the same processes in the epsilonproteobacteria. Instead, these bacteria often display extensive variation in common biological mechanisms relative to those of other prototypical bacteria. In this review, five biological processes of commonly studied model bacterial species are compared to those of the epsilonproteobacteria C. jejuni and H. pylori. Distinct differences in the processes of flagellar biosynthesis, DNA uptake and recombination, iron homeostasis, interaction with epithelial cells, and protein glycosylation are highlighted. Collectively, these studies support a broader view of the vast repertoire of biological mechanisms employed by bacteria and suggest that future studies of the epsilonproteobacteria will continue to provide novel and interesting information regarding prokaryotic cellular biology. PMID:21372321

Community and ecosystem effects of intraspecific genetic diversity in grassland microcosms of varying species diversity.

PubMed

Fridley, Jason D; Grime, J Philip

2010-08-01

Studies of whether plant community structure and ecosystem properties depend on the genetic diversity of component populations have been largely restricted to species monocultures and have involved levels of genetic differentiation that do not necessarily correspond to that exhibited by neighboring mature individuals in the field. We established experimental communities of varying intraspecific genetic diversity, using genotypes of eight species propagated from clonal material of individuals derived from a small (100-m2) limestone grassland community, and tested whether genetic diversity (one, four, and eight genotypes per species) influenced community composition and annual aboveground productivity across communities of one, four, and eight species. Eight-species communities were represented by common grass, sedge, and forb species, and four- and one-species communities were represented by four graminoids and the dominant grass Festuca ovina, respectively. After three years of community development, there was a marginal increase of species diversity with increased genetic diversity in four- and eight-species communities, and genetic diversity altered the performance of genotypes in monospecific communities of F. ovina. However, shifts in composition from genetic diversity were not sufficient to alter patterns of community productivity. Neighborhood models describing pairwise interactions between species indicated that genetic diversity decreased the intensity of competition between species in four-species mixtures, thereby promoting competitive equivalency and enhancing species equitability. In F. ovina monocultures, neighborhood models revealed both synergistic and antagonistic interactions between genotypes that were reduced in intensity on more stressful shallow soils. Although the dependence of F. ovina genotype performance on neighborhood genetic composition did not influence total productivity, such dependence was sufficient to uncouple genotype performance

Identification of Helicobacter spp. in bile and gallbladder tissue of patients with symptomatic gallbladder disease

PubMed Central

Sabbaghian, M Shirin; Ranaudo, Jeffrey; Zeng, Lin; Alongi, Alexandra P; Perez-Perez, Guillermo; Shamamian, Peter

2010-01-01

Background: This experimental study was designed to determine if Helicobacter spp. contribute to benign gallbladder disease using polymerase chain reaction (PCR) methods. Methods: Patients with benign gallbladder disease scheduled for elective cholecystectomy at New York University Langone Medical Center were recruited from February to May 2008. Bile, gallbladder tissue and gallstones were collected. DNA was isolated from these specimens and amplified via PCR using C97F and C98R primers specific for Helicobacter spp. Appropriate positive and negative controls were used. Products were analysed with agarose gel electrophoresis, sequenced and results aligned using sequencher. Plasma was collected for detection of anti-Helicobacter pylori antibodies via enzyme-linked immunosorbent assay. Results: Of 36 patients, 12 patients' bile and/or tissue were positive for Helicobacter spp. by PCR. Species were most homologous with H. pylori, although other Helicobacter spp. were suggested. Six of 12 patients demonstrated anti-Helicobacter antibodies in plasma, suggesting that the remaining six might have demonstrated other species besides H. pylori. Four of six plasma samples with anti-Helicobacter antibodies were anti-CagA (cytotoxin associated gene) negative. Discussion: Helicobacter spp. can be detected in bile and gallbladder tissue of patients with benign gallbladder disease. The contribution of these bacteria to the pathophysiology of gallbladder disease and gallstone formation requires further study. PMID:20495657

Co-infection of the Siberian hamster (Phodopus sungorus) with a novel Helicobacter sp. and Campylobacter sp.

PubMed

Nagamine, Claude M; Shen, Zeli; Luong, Richard H; McKeon, Gabriel P; Ruby, Norman F; Fox, James G

2015-05-01

We report the isolation of a novel helicobacter isolated from the caecum of the Siberian hamster (Phodopus sungorus). Sequence analysis showed 97% sequence similarity to Helicobacter ganmani. In addition, we report the co-infection of these Siberian hamsters with a Campylobacter sp. and a second Helicobacter sp. with 99% sequence similarity to Helicobacter sp. flexispira taxon 8 (Helicobacter bilis), a species isolated previously from patients with bacteraemia. Gross necropsy and histopathology did not reveal any overt pathological lesions of the liver and gastrointestinal tract that could be attributed to the Helicobacter or Campylobacter spp. infections. This is the first helicobacter to be identified in the Siberian hamster and the first report of co-infection of Helicobacter spp. and Campylobacter sp. in asymptomatic Siberian hamsters. © 2015 The Authors.

Co-infection of the Siberian hamster (Phodopus sungorus) with a novel Helicobacter sp. and Campylobacter sp.

PubMed Central

Shen, Zeli; Luong, Richard H.; McKeon, Gabriel P.; Ruby, Norman F.; Fox, James G.

2015-01-01

We report the isolation of a novel helicobacter isolated from the caecum of the Siberian hamster (Phodopus sungorus). Sequence analysis showed 97 % sequence similarity to Helicobacter ganmani. In addition, we report the co-infection of these Siberian hamsters with a Campylobacter sp. and a second Helicobacter sp. with 99 % sequence similarity to Helicobacter sp. flexispira taxon 8 (Helicobacter bilis), a species isolated previously from patients with bacteraemia. Gross necropsy and histopathology did not reveal any overt pathological lesions of the liver and gastrointestinal tract that could be attributed to the Helicobacter or Campylobacter spp. infections. This is the first helicobacter to be identified in the Siberian hamster and the first report of co-infection of Helicobacter spp. and Campylobacter sp. in asymptomatic Siberian hamsters. PMID:25752854

Genomic patterns of species diversity and divergence in Eucalyptus.

PubMed

Hudson, Corey J; Freeman, Jules S; Myburg, Alexander A; Potts, Brad M; Vaillancourt, René E

2015-06-01

We examined genome-wide patterns of DNA sequence diversity and divergence among six species of the important tree genus Eucalyptus and investigated their relationship with genomic architecture. Using c. 90 range-wide individuals of each Eucalyptus species (E. grandis, E. urophylla, E. globulus, E. nitens, E. dunnii and E. camaldulensis), genetic diversity and divergence were estimated from 2840 polymorphic diversity arrays technology markers covering the 11 chromosomes. Species differentiating markers (SDMs) identified in each of 15 pairwise species comparisons, along with species diversity (HHW ) and divergence (FST ), were projected onto the E. grandis reference genome. Across all species comparisons, SDMs totalled 1.1-5.3% of markers and were widely distributed throughout the genome. Marker divergence (FST and SDMs) and diversity differed among and within chromosomes. Patterns of diversity and divergence were broadly conserved across species and significantly associated with genomic features, including the proximity of markers to genes, the relative number of clusters of tandem duplications, and gene density within or among chromosomes. These results suggest that genomic architecture influences patterns of species diversity and divergence in the genus. This influence is evident across the six species, encompassing diverse phylogenetic lineages, geography and ecology. © 2015 University of Tasmania New Phytologist © 2015 New Phytologist Trust.

Helicobacter marmotae sp. nov. isolated from livers of woodchucks and intestines of cats.

PubMed

Fox, James G; Shen, Zeli; Xu, Shilu; Feng, Yan; Dangler, Charles A; Dewhirst, Floyd E; Paster, Bruce J; Cullen, John M

2002-07-01

Woodchucks (Marmota monax) have a high incidence of hepatocellular carcinoma (HCC) associated with chronic infection with woodchuck hepatitis virus (WHV) and serve as a model of hepatitis B virus-associated HCC in humans. Helicobacter hepaticus, an enterohepatic helicobacter in mice, is known to cause hepatocellular adenomas and carcinomas in susceptible mouse strains. In long-term chemical bioassays conducted with B6C3F(1) mice, H. hepaticus has been regarded as a confounding factor because of its tumor-promoting activity. In order to determine if woodchucks harbor a Helicobacter sp. that might play a role in potentiating hepatic inflammation or neoplasia, a study was undertaken to determine whether woodchucks' livers were infected with a Helicobacter sp. Frozen liver samples from 20 (17 WHV-infected and 3 noninfected) woodchucks, 10 with WHV-associated hepatic tumors and 10 without tumors, were cultured by microaerobic techniques and analyzed by using genus- and species-specific helicobacter PCR primers. A 1,200-bp Helicobacter sp.-specific sequence was amplified from 14 liver samples. Southern hybridization confirmed the specific identity of the PCR products. Nine of the 10 livers with tumors had positive Helicobacter sp. identified by PCR, whereas 5 of the 10 livers without tumors were positive. By use of 16S rRNA species-specific primers for H. marmotae, two additional liver samples from the nontumor group had positive PCR amplicons confirmed by Southern hybridization. A urease-, catalase-, and oxidase-positive bacterium was isolated from one liver sample from a liver tumor-positive woodchuck. By 16S rRNA analysis and biochemical and phenotypic characteristics, the organism was classified as a novel Helicobacter sp. Subsequently, four additional bacterial strains isolated from feces of cats and characterized by biochemical, phenotypic, and 16S rRNA analysis were determined to be identical to the woodchuck isolate. We propose the name Helicobacter marmotae sp

Helicobacter marmotae sp. nov. Isolated from Livers of Woodchucks and Intestines of Cats

PubMed Central

Fox, James G.; Shen, Zeli; Xu, Shilu; Feng, Yan; Dangler, Charles A.; Dewhirst, Floyd E.; Paster, Bruce J.; Cullen, John M.

2002-01-01

Woodchucks (Marmota monax) have a high incidence of hepatocellular carcinoma (HCC) associated with chronic infection with woodchuck hepatitis virus (WHV) and serve as a model of hepatitis B virus-associated HCC in humans. Helicobacter hepaticus, an enterohepatic helicobacter in mice, is known to cause hepatocellular adenomas and carcinomas in susceptible mouse strains. In long-term chemical bioassays conducted with B6C3F1 mice, H. hepaticus has been regarded as a confounding factor because of its tumor-promoting activity. In order to determine if woodchucks harbor a Helicobacter sp. that might play a role in potentiating hepatic inflammation or neoplasia, a study was undertaken to determine whether woodchucks' livers were infected with a Helicobacter sp. Frozen liver samples from 20 (17 WHV-infected and 3 noninfected) woodchucks, 10 with WHV-associated hepatic tumors and 10 without tumors, were cultured by microaerobic techniques and analyzed by using genus- and species-specific helicobacter PCR primers. A 1,200-bp Helicobacter sp.-specific sequence was amplified from 14 liver samples. Southern hybridization confirmed the specific identity of the PCR products. Nine of the 10 livers with tumors had positive Helicobacter sp. identified by PCR, whereas 5 of the 10 livers without tumors were positive. By use of 16S rRNA species-specific primers for H. marmotae, two additional liver samples from the nontumor group had positive PCR amplicons confirmed by Southern hybridization. A urease-, catalase-, and oxidase-positive bacterium was isolated from one liver sample from a liver tumor-positive woodchuck. By 16S rRNA analysis and biochemical and phenotypic characteristics, the organism was classified as a novel Helicobacter sp. Subsequently, four additional bacterial strains isolated from feces of cats and characterized by biochemical, phenotypic, and 16S rRNA analysis were determined to be identical to the woodchuck isolate. We propose the name Helicobacter marmotae sp

Mouririelliptica: validation of gastroprotective, healing and anti-Helicobacter pylori effects.

PubMed

Moleiro, Fábio Cruz; Andreo, Márcio Aparecido; Santos, Raquel de Cássia Dos; Moraes, Thiago de Mello; Rodrigues, Clenilson Martins; Carli, Camila Bernardes de Andrade; Lopes, Flávia Cristine Mascia; Pellizzon, Cláudia Helena; Carlos, Iracilda Zeppone; Bauab, Tais Maria; Vilegas, Wagner; Hiruma-Lima, Clélia Akiko

2009-06-25

Mouriri elliptica Martius (Melastomataceae) is species reputed in folk medicine to heal gastric ulcer and gastritis. Methanolic extract (ME) and ethyl acetate fraction (EAF) from leaves of Mouriri elliptica were evaluated for their gastroprotective, healing, immunological, toxicological and anti-Helicobacter pylori activities. The gastroprotective action of ME and EAF was evaluated in rodent experimental models and to elucidate mechanisms of action, the antisecretory action, involvements of NO, SH, PGE(2), anti-Helicobacter pylori action of ME was evaluated. We also used immunohistochemical (PCNA and COX-2) and immunomodulatory (murine peritoneal macrophages) assays to evaluate Mouriri elliptica effects. ME present gastroprotective action without antisecretory effect. Otherwise, ME showed anti-Helicobacter pylori action (MIC=0.025mug/mL) and was able to inhibit NO production by macrophages. This species also accelerate the healing of ulcerated gastric mucosa by stimulating proliferation factors (PCNA), COX-2 and maintained basal PGE(2) level independent action of NSAID in gastric mucosa. The phytochemical investigation showed that this species possesses phenolic acid derivatives, acylglycoflavonoids and condensed tannins which probably influenced their pharmacological action. All these results suggest the efficacy and safety of Mouriri elliptica in combating and healing gastric ulcer.

Species Pool Functional Diversity Plays a Hidden Role in Generating β-Diversity.

PubMed

Patrick, Christopher J; Brown, Bryan L

2018-05-01

Functional trait diversity is used as a way to infer mechanistic processes that drive community assembly. While functional diversity within communities is often viewed as a response variable, here we present and test a framework for how functional diversity among taxa in the regional species pool drives the assembly of communities among habitats. We predicted that species pool functional diversity should work with environmental heterogeneity to drive β-diversity. We tested these predictions by modeling empirical patterns in invertebrate communities from 570 streams in 52 watersheds. Our analysis of the field data provided strong support for the inclusion of both functional diversity and environmental heterogeneity in the models, and our predictions were supported when the community was analyzed all together. However, analyses within individual functional feeding guilds revealed strong context dependency in the relative importance of functional diversity, γ-richness, and environmental heterogeneity to β-diversity. We interpret the results to mean that functional diversity can play an important role in driving β-diversity; however, within guilds the nature of interspecific interactions and species pool size complicate the relationship. Future research should test this conceptual model across different ecosystems and in experimental settings using metacommunity mesocosms to enhance our understanding of the role that functional variation plays in generating spatial biodiversity patterns.

Plant Functional Diversity and Species Diversity in the Mongolian Steppe

PubMed Central

Liu, Guofang; Xie, Xiufang; Ye, Duo; Ye, Xuehua; Tuvshintogtokh, Indree; Mandakh, Bayart; Huang, Zhenying; Dong, Ming

2013-01-01

Background The Mongolian steppe is one of the most important grasslands in the world but suffers from aridization and damage from anthropogenic activities. Understanding structure and function of this community is important for the ecological conservation, but has seldom been investigated. Methodology/Principal Findings In this study, a total of 324 quadrats located on the three main types of Mongolian steppes were surveyed. Early-season perennial forbs (37% of total importance value), late-season annual forbs (33%) and late-season perennial forbs (44%) were dominant in meadow, typical and desert steppes, respectively. Species richness, diversity and plant functional type (PFT) richness decreased from the meadow, via typical to desert steppes, but evenness increased; PFT diversity in the desert and meadow steppes was higher than that in typical steppe. However, above-ground net primary productivity (ANPP) was far lower in desert steppe than in the other two steppes. In addition, the slope of the relationship between species richness and PFT richness increased from the meadow, via typical to desert steppes. Similarly, with an increase in species diversity, PFT diversity increased more quickly in both the desert and typical steppes than that in meadow steppe. Random resampling suggested that this coordination was partly due to a sampling effect of diversity. Conclusions/Significance These results indicate that desert steppe should be strictly protected because of its limited functional redundancy, which its ecological functioning is sensitive to species loss. In contrast, despite high potential forage production shared by the meadow and typical steppes, management of these two types of steppes should be different: meadow steppe should be preserved due to its higher conservation value characterized by more species redundancy and higher spatial heterogeneity, while typical steppe could be utilized moderately because its dominant grass genus Stipa is resistant to

Helicobacter-negative gastritis: a distinct entity unrelated to Helicobacter pylori infection.

PubMed

Genta, R M; Sonnenberg, A

2015-01-01

Helicobacter-negative gastritis is diagnosed when no organisms are detected in a gastric mucosa with typical features of Helicobacter gastritis (Hp-gastritis). If Helicobacter-negative gastritis consisted mostly of 'missed' Helicobacter infections, its prevalence should represent a constant percentage of these infections in a population, and their clinico-epidemiological features would overlap. To compare the epidemiologic patterns of Hp-positive and Hp-negative gastritis. From a pathology database, we extracted demographic, clinical and histopathological data from patients with gastric biopsies (1.2008-12.2013). We allocated patients to high (≥12%) and low (≤6%) H. pylori prevalence regions defined by ZIP code-based data. The prevalence of H. pylori-positive and -negative gastritis by sex, age and state were expressed as a per cent of the total study population stratified accordingly. Of 895 323 patients, 10.6% had Hp-gastritis and 1.5% Helicobacter-negative gastritis. Hp-gastritis, but not Helicobacter-negative gastritis, was more common in males than females (OR 1.17, 95% CI: 1.16-1.19). While Hp-gastritis was more prevalent in high than in low-prevalence areas (OR 3.65, 95% CI: 3.57-3.74), Helicobacter-negative gastritis was only minimally affected by the underlying H. pylori prevalence (1.7% vs. 1.5%). The age-specific prevalence of Hp-gastritis peaked in the 4th to 5th decades; Helicobacter-negative gastritis exhibited a low and relatively flat pattern. The geographic distribution of H. pylori-positive and -negative gastritis showed no significant correlation. Intestinal metaplasia was found in 13.0% of patients with Hp-gastritis and in 6.1% of those with Helicobacter-negative gastritis (OR 0.43, 95% CI: 0.40-0.47). These data suggest that Helicobacter-negative gastritis is, in the vast majority of cases, a nosologically and epidemiologically distinct entity that deserves further investigation. © 2014 John Wiley & Sons Ltd.

Inventory, differentiation, and proportional diversity: a consistent terminology for quantifying species diversity.

PubMed

Jurasinski, Gerald; Retzer, Vroni; Beierkuhnlein, Carl

2009-02-01

Almost half a century after Whittaker (Ecol Monogr 30:279-338, 1960) proposed his influential diversity concept, it is time for a critical reappraisal. Although the terms alpha, beta and gamma diversity introduced by Whittaker have become general textbook knowledge, the concept suffers from several drawbacks. First, alpha and gamma diversity share the same characteristics and are differentiated only by the scale at which they are applied. However, as scale is relative--depending on the organism(s) or ecosystems investigated--this is not a meaningful ecological criterion. Alpha and gamma diversity can instead be grouped together under the term "inventory diversity." Out of the three levels proposed by Whittaker, beta diversity is the one which receives the most contradictory comments regarding its usefulness ("key concept" vs. "abstruse concept"). Obviously beta diversity means different things to different people. Apart from the large variety of methods used to investigate it, the main reason for this may be different underlying data characteristics. A literature review reveals that the multitude of measures used to assess beta diversity can be sorted into two conceptually different groups. The first group directly takes species distinction into account and compares the similarity of sites (similarity indices, slope of the distance decay relationship, length of the ordination axis, and sum of squares of a species matrix). The second group relates species richness (or other summary diversity measures) of two (or more) different scales to each other (additive and multiplicative partitioning). Due to that important distinction, we suggest that beta diversity should be split into two levels, "differentiation diversity" (first group) and "proportional diversity" (second group). Thus, we propose to use the terms "inventory diversity" for within-sample diversity, "differentiation diversity" for compositional similarity between samples, and "proportional diversity" for the

Measuring β-diversity with species abundance data.

PubMed

Barwell, Louise J; Isaac, Nick J B; Kunin, William E

2015-07-01

In 2003, 24 presence-absence β-diversity metrics were reviewed and a number of trade-offs and redundancies identified. We present a parallel investigation into the performance of abundance-based metrics of β-diversity. β-diversity is a multi-faceted concept, central to spatial ecology. There are multiple metrics available to quantify it: the choice of metric is an important decision. We test 16 conceptual properties and two sampling properties of a β-diversity metric: metrics should be 1) independent of α-diversity and 2) cumulative along a gradient of species turnover. Similarity should be 3) probabilistic when assemblages are independently and identically distributed. Metrics should have 4) a minimum of zero and increase monotonically with the degree of 5) species turnover, 6) decoupling of species ranks and 7) evenness differences. However, complete species turnover should always generate greater values of β than extreme 8) rank shifts or 9) evenness differences. Metrics should 10) have a fixed upper limit, 11) symmetry (βA,B  = βB,A ), 12) double-zero asymmetry for double absences and double presences and 13) not decrease in a series of nested assemblages. Additionally, metrics should be independent of 14) species replication 15) the units of abundance and 16) differences in total abundance between sampling units. When samples are used to infer β-diversity, metrics should be 1) independent of sample sizes and 2) independent of unequal sample sizes. We test 29 metrics for these properties and five 'personality' properties. Thirteen metrics were outperformed or equalled across all conceptual and sampling properties. Differences in sensitivity to species' abundance lead to a performance trade-off between sample size bias and the ability to detect turnover among rare species. In general, abundance-based metrics are substantially less biased in the face of undersampling, although the presence-absence metric, βsim , performed well overall. Only �

Sierra Nevada meadows: species alpha diversity

Treesearch

Raymond D. Ratliff

1993-01-01

Plant species diversity refers to variety and abundance; it does not necessarily relate to meadow health but may provide information important in an ecosystem context. Monitoring to detect change in diversity usually begins with estimating alpha (within) diversity of plant communities. Because few such estimates exist for meadow site classes or specific sites of the...

Helicobacter pylori Heat Shock Protein A: Serologic Responses and Genetic Diversity

PubMed Central

Ng, Enders K. W.; Thompson, Stuart A.; Pérez-Pérez, Guillermo I.; Kansau, Imad; van der Ende, Arie; Labigne, Agnès; Sung, Joseph J. Y.; Chung, S. C. Sydney; Blaser, Martin J.

1999-01-01

Helicobacter pylori synthesizes an unusual GroES homolog, heat shock protein A (HspA). The present study was aimed at an assessment of the serological response to HspA in a group of Chinese patients with defined gastroduodenal pathologies and determination of whether diversity is present in the nucleotide sequences encoding HspA in isolates from these patients. Serum samples collected from 154 patients who had an upper gastrointestinal pathology and the presence of H. pylori defined by biopsy were tested for an immunoglobulin G (IgG) serologic response to H. pylori HspA by an enzyme linked immunosorbant assay. HspA-encoding nucleotide sequences in H. pylori isolates from 14 patients (7 seropositive and 7 seronegative for HspA) were analyzed by PCR and direct sequencing of the PCR products. The sequencing results were compared to those of 48 isolates from other parts of the world. Of the 154 known H. pylori-positive patients, 54 (35.1%) were seropositive for HspA. The A domain (GroES homology) of HspA was highly conserved in the 14 isolates tested. Although the B domain (metal-binding site unique to H. pylori) resembled that in the known major variant, particular amino acid substitutions allowed definition of an HspA variant associated with isolates from East Asia. There were no associations between patient characteristics and HspA seropositivity or amino acid sequences. We confirmed in this study that the clinical outcomes of H. pylori infection are not related to HspA antigenicity or to sequence variation. However, B-domain sequence variation may be a marker for the study of the genetic diversity of H. pylori strains of different geographic origins. PMID:10225839

Recent "omics" advances in Helicobacter pylori.

PubMed

Berthenet, Elvire; Sheppard, Sam; Vale, Filipa F

2016-09-01

The development of high-throughput whole genome sequencing (WGS) technologies is changing the face of microbiology, facilitating the comparison of large numbers of genomes from different lineages of a same organism. Our aim was to review the main advances on Helicobacter pylori "omics" and to understand how this is improving our knowledge of the biology, diversity and pathogenesis of H. pylori. Since the first H. pylori isolate was sequenced in 1997, 510 genomes have been deposited in the NCBI archive, providing a basis for improved understanding of the epidemiology and evolution of this important pathogen. This review focuses on works published between April 2015 and March 2016. Helicobacter "omics" is already making an impact and is a growing research field. Ultimately these advances will be translated into a routine clinical laboratory setting in order to improve public health. © 2016 John Wiley & Sons Ltd.

Species diversity: Benthonic Foraminifera in Western North Atlantic

USGS Publications Warehouse

Buzas, M.A.; Gibson, T.G.

1969-01-01

Maximum species diversity occurs at abyssal depths of greater than 2500 meters. Other diversity peaks occur at depths of 35 to 45 meters and 100 to 200 meters. The peak at 35 to 45 meters is due to species equitability, whereas the other two peaks correspond to an increase in the number of species.

Review: Impact of Helicobacter pylori on Alzheimer's disease: What do we know so far?

PubMed

Doulberis, Michael; Kotronis, Georgios; Thomann, Robert; Polyzos, Stergios A; Boziki, Marina; Gialamprinou, Dimitra; Deretzi, Georgia; Katsinelos, Panagiotis; Kountouras, Jannis

2018-02-01

Helicobacter pylori has changed radically gastroenterologic world, offering a new concept in patients' management. Over time, more medical data gave rise to diverse distant, extragastric manifestations and interactions of the "new" discovered bacterium. Special interest appeared within the field of neurodegenerative diseases and particularly Alzheimer's disease, as the latter and Helicobacter pylori infection are associated with a large public health burden and Alzheimer's disease ranks as the leading cause of disability. However, the relationship between Helicobacter pylori infection and Alzheimer's disease remains uncertain. We performed a narrative review regarding a possible connection between Helicobacter pylori and Alzheimer's disease. All accessible relevant (pre)clinical studies written in English were included. Both affected pathologies were briefly analyzed, and relevant studies are discussed, trying to focus on the possible pathogenetic role of this bacterium in Alzheimer's disease. Data stemming from both epidemiologic studies and animal experiments seem to be rather encouraging, tending to confirm the hypothesis that Helicobacter pylori infection might influence the course of Alzheimer's disease pleiotropically. Possible main mechanisms may include the bacterium's access to the brain via the oral-nasal-olfactory pathway or by circulating monocytes (infected with Helicobacter pylori due to defective autophagy) through disrupted blood-brain barrier, thereby possibly triggering neurodegeneration. Current data suggest that Helicobacter pylori infection might influence the pathophysiology of Alzheimer's disease. However, further large-scale randomized controlled trials are mandatory to clarify a possible favorable effect of Helicobacter pylori eradication on Alzheimer's disease pathophysiology, before the recommendation of short-term and cost-effective therapeutic regimens against Helicobacter pylori-related Alzheimer's disease. © 2017 John Wiley & Sons

Soil properties drive a negative correlation between species diversity and genetic diversity in a tropical seasonal rainforest

PubMed Central

Xu, Wumei; Liu, Lu; He, Tianhua; Cao, Min; Sha, Liqing; Hu, Yuehua; Li, Qiaoming; Li, Jie

2016-01-01

A negative species-genetic diversity correlation (SGDC) could be predicted by the niche variation hypothesis, whereby an increase in species diversity within community reduces the genetic diversity of the co-occurring species because of the reduction in average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of the species within community. We tested these predictions within a 20 ha tropical forest dynamics plot (FDP) in the Xishuangbanna tropical seasonal rainforest. We established 15 plots within the FDP and investigated the soil properties, tree diversity, and genetic diversity of a common tree species Beilschmiedia roxburghiana within each plot. We observed a significant negative correlation between tree diversity and the genetic diversity of B. roxburghiana within the communities. Using structural equation modeling, we further determined that the inter-plot environmental characteristics (soil pH and phosphorus availability) directly affected tree diversity and that the tree diversity within the community determined the genetic diversity of B. roxburghiana. Increased soil pH and phosphorus availability might promote the coexistence of more tree species within community and reduce genetic diversity of B. roxburghiana for the reduced average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of B. roxburghiana within community. PMID:26860815

Soil properties drive a negative correlation between species diversity and genetic diversity in a tropical seasonal rainforest.

PubMed

Xu, Wumei; Liu, Lu; He, Tianhua; Cao, Min; Sha, Liqing; Hu, Yuehua; Li, Qiaoming; Li, Jie

2016-02-10

A negative species-genetic diversity correlation (SGDC) could be predicted by the niche variation hypothesis, whereby an increase in species diversity within community reduces the genetic diversity of the co-occurring species because of the reduction in average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of the species within community. We tested these predictions within a 20 ha tropical forest dynamics plot (FDP) in the Xishuangbanna tropical seasonal rainforest. We established 15 plots within the FDP and investigated the soil properties, tree diversity, and genetic diversity of a common tree species Beilschmiedia roxburghiana within each plot. We observed a significant negative correlation between tree diversity and the genetic diversity of B. roxburghiana within the communities. Using structural equation modeling, we further determined that the inter-plot environmental characteristics (soil pH and phosphorus availability) directly affected tree diversity and that the tree diversity within the community determined the genetic diversity of B. roxburghiana. Increased soil pH and phosphorus availability might promote the coexistence of more tree species within community and reduce genetic diversity of B. roxburghiana for the reduced average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of B. roxburghiana within community.

Helicobacter pylori-induced gastric pathology: insights from in vivo and ex vivo models

PubMed Central

Williams, Jonathan M.

2017-01-01

ABSTRACT Gastric colonization with Helicobacter pylori induces diverse human pathological conditions, including superficial gastritis, peptic ulcer disease, mucosa-associated lymphoid tissue (MALT) lymphoma, and gastric adenocarcinoma and its precursors. The treatment of these conditions often relies on the eradication of H. pylori, an intervention that is increasingly difficult to achieve and that does not prevent disease progression in some contexts. There is, therefore, a pressing need to develop new experimental models of H. pylori-associated gastric pathology to support novel drug development in this field. Here, we review the current status of in vivo and ex vivo models of gastric H. pylori colonization, and of Helicobacter-induced gastric pathology, focusing on models of gastric pathology induced by H. pylori, Helicobacter felis and Helicobacter suis in rodents and large animals. We also discuss the more recent development of gastric organoid cultures from murine and human gastric tissue, as well as from human pluripotent stem cells, and the outcomes of H. pylori infection in these systems. PMID:28151409

Assessing Species Diversity Using Metavirome Data: Methods and Challenges.

PubMed

Herath, Damayanthi; Jayasundara, Duleepa; Ackland, David; Saeed, Isaam; Tang, Sen-Lin; Halgamuge, Saman

2017-01-01

Assessing biodiversity is an important step in the study of microbial ecology associated with a given environment. Multiple indices have been used to quantify species diversity, which is a key biodiversity measure. Measuring species diversity of viruses in different environments remains a challenge relative to measuring the diversity of other microbial communities. Metagenomics has played an important role in elucidating viral diversity by conducting metavirome studies; however, metavirome data are of high complexity requiring robust data preprocessing and analysis methods. In this review, existing bioinformatics methods for measuring species diversity using metavirome data are categorised broadly as either sequence similarity-dependent methods or sequence similarity-independent methods. The former includes a comparison of DNA fragments or assemblies generated in the experiment against reference databases for quantifying species diversity, whereas estimates from the latter are independent of the knowledge of existing sequence data. Current methods and tools are discussed in detail, including their applications and limitations. Drawbacks of the state-of-the-art method are demonstrated through results from a simulation. In addition, alternative approaches are proposed to overcome the challenges in estimating species diversity measures using metavirome data.

Species richness and morphological diversity of passerine birds

PubMed Central

Ricklefs, Robert E.

2012-01-01

The relationship between species richness and the occupation of niche space can provide insight into the processes that shape patterns of biodiversity. For example, if species interactions constrained coexistence, one might expect tendencies toward even spacing within niche space and positive relationships between diversity and total niche volume. I use morphological diversity of passerine birds as a proxy for diet, foraging maneuvers, and foraging substrates and examine the morphological space occupied by regional and local passerine avifaunas. Although independently diversified regional faunas exhibit convergent morphology, species are clustered rather than evenly distributed, the volume of the morphological space is weakly related to number of species per taxonomic family, and morphological volume is unrelated to number of species within both regional avifaunas and local assemblages. These results seemingly contradict patterns expected when species interactions constrain regional or local diversity, and they suggest a larger role for diversification, extinction, and dispersal limitation in shaping species richness. PMID:22908271

Survey of Helicobacter infection in domestic and feral cats in Korea

PubMed Central

Ghil, Heh-Myung; Yoo, Jong-Hyeon; Jung, Woo-Sung; Chung, Tae-Ho; Youn, Hwa-Young

2009-01-01

Discovery of Helicobacter (H.) pylori has led to a fundamental change in our understanding of gastric diseases in humans. Previous studies have found various Helicobacter spp. in dogs and cats, and pets have been questioned as a zoonotic carrier. The present study surveyed the Helicobacter infections and investigated the presence of H. felis and H. pylori infections in domestic and feral cats in Korea. Sixty-four domestic cats and 101 feral cats were selected from an animal shelter. Saliva and feces were evaluated by Helicobacter genus-specific polymerase chain reaction (PCR). Genus-specific PCR positive samples were further evaluated for H. felis and H. pylori using specific primer pairs. Thirty-six of 64 (56.3%) samples from domestic cats and 92 of 101 (91.1%) samples from feral cats were PCR positive; the positive rate of feces samples was higher than that of saliva samples in both groups. H. felis and H. pylori species-specific PCR was uniformly negative. The prevalence of Helicobacter spp. in feral cats was approximately two-fold higher than that of domestic cats. The fecal-oral route may be more a common transmission route not only between cats but also in humans. PMID:19255526

Survey of Helicobacter infection in domestic and feral cats in Korea.

PubMed

Ghil, Heh-Myung; Yoo, Jong-Hyeon; Jung, Woo-Sung; Chung, Tae-Ho; Youn, Hwa-Young; Hwang, Cheol-Yong

2009-03-01

Discovery of Helicobacter (H.) pylori has led to a fundamental change in our understanding of gastric diseases in humans. Previous studies have found various Helicobacter spp. in dogs and cats, and pets have been questioned as a zoonotic carrier. The present study surveyed the Helicobacter infections and investigated the presence of H. felis and H. pylori infections in domestic and feral cats in Korea. Sixty-four domestic cats and 101 feral cats were selected from an animal shelter. Saliva and feces were evaluated by Helicobacter genus-specific polymerase chain reaction (PCR). Genus-specific PCR positive samples were further evaluated for H. felis and H. pylori using specific primer pairs. Thirty-six of 64 (56.3%) samples from domestic cats and 92 of 101 (91.1%) samples from feral cats were PCR positive; the positive rate of feces samples was higher than that of saliva samples in both groups. H. felis and H. pylori species-specific PCR was uniformly negative. The prevalence of Helicobacter spp. in feral cats was approximately two-fold higher than that of domestic cats. The fecal-oral route may be more a common transmission route not only between cats but also in humans.

Genetic affinities of Helicobacter pylori isolates from ethnic Arabs in Kuwait

PubMed Central

2010-01-01

Helicobacter pylori is one of the most genetically diverse of bacterial species, and since the 5'-end of cagA gene and the middle allele of vacA gene of H. pylori from different populations exhibit considerable polymorphisms, these sequence diversities were used to gain insights into the genetic affinities of this gastric pathogen from different populations. Because the genetic affinity of Arab strains from the Arabian Gulf is not known, we carried out genetic analysis based on sequence diversities of the cagA and the vacA genes of H. pylori from 9 ethnic Arabs in Kuwait. The analysis showed that the Kuwaiti isolates are closely related to the Indo-European group of strains, although some strains have a tendency to form a separate cluster close to the Indo- European group, but clearly distinct from East Asian strains. However, these results need to be confirmed by analyses of neutral markers (house-keeping genes in a multi-locus sequence typing [MLST]) platform. The profiling of virulence-associated genes may have resulted from ecologically distinct populations due to human migration and geographical separation over long periods of time. PMID:20602767

Size and species diversity of zooplankton communities in fluctuating Mediterranean salt marshes

NASA Astrophysics Data System (ADS)

Brucet, Sandra; Boix, Dani; López-Flores, Rocío; Badosa, Anna; Quintana, Xavier D.

2006-04-01

Differences in size and species diversity were analysed in a zooplankton community of a Mediterranean salt marsh (Empordà wetlands, NE Iberian Peninsula), where the dominance of a single species was frequent. In the permanent salt marsh, species diversity and size diversity had similar patterns along zooplankton succession. In the temporary salt marsh species diversity was high after flooding and diminished once water inputs ceased. As species diversity declined size diversity increased. Eventually, one species of calanoid dominated the zooplankton community. The high size diversity in situations of calanoid dominance was possibly due to the co-occurrence of different developmental stages, each of which have different diets. Size diversity would thus indicate trophic niche segregation among different sizes. The combined use of species and size diversity values allows the identification of the successional phases.

Origin matters: diversity affects the performance of alien invasive species but not of native species.

PubMed

Sun, Yan; Müller-Schärer, Heinz; Maron, John L; Schaffner, Urs

2015-06-01

At local scales, it has often been found that invasibility decreases with increasing resident plant diversity. However, whether resident community diversity similarly resists invasion by alien versus native species is seldom studied. We examined this issue by invading constructed native plant assemblages that varied in species and functional richness with invasive alien or native Asteraceae species. Assemblages were also invaded with spotted knapweed, Centaurea stoebe, a native European aster that has been previously used in diversity-invasibility experiments in North America. We also conducted a field survey to explore the generality of the patterns generated from our experimental study. Both experimental and observational work revealed that increasing diversity reduced the performance of alien but not native invaders. Centaurea stoebe invading its native community performed poorly regardless of resident diversity, whereas in a parallel, previously published study conducted in North America, C. stoebe easily invaded low-diversity but not high-diversity assemblages. Our results suggest that diversity is an attribute of resident communities that makes them more or less susceptible to invasion by novel invasive alien but not native plant species.

Resource diversity and provenance underpin spatial patterns in functional diversity across native and exotic species.

PubMed

Méndez, Verónica; Wood, Jamie R; Butler, Simon J

2018-05-01

Functional diversity metrics are increasingly used to augment or replace taxonomic diversity metrics to deliver more mechanistic insights into community structure and function. Metrics used to describe landscape structure and characteristics share many of the same limitations as taxonomy-based metrics, particularly their reliance on anthropogenically defined typologies with little consideration of structure, management, or function. However, the development of alternative metrics to describe landscape characteristics has been limited. Here, we extend the functional diversity framework to characterize landscapes based on the diversity of resources available across habitats present. We then examine the influence of resource diversity and provenance on the functional diversities of native and exotic avian communities in New Zealand. Invasive species are increasingly prevalent and considered a global threat to ecosystem function, but the characteristics of and interactions between sympatric native and exotic communities remain unresolved. Understanding their comparative responses to environmental change and the mechanisms underpinning them is of growing importance in predicting community dynamics and changing ecosystem function. We use (i) matrices of resource use (species) and resource availability (habitats) and (ii) occurrence data for 62 native and 25 exotic species and 19 native and 13 exotic habitats in 2015 10 × 10 km quadrats to examine the relationship between native and exotic avian and landscape functional diversity. The numbers of species in, and functional diversities of, native and exotic communities were positively related. Each community displayed evidence of environmental filtering, but it was significantly stronger for exotic species. Less environmental filtering occurred in landscapes providing a more diverse combination of resources, with resource provenance also an influential factor. Landscape functional diversity explained a greater

Testing the mechanisms of diversity-dependent overyielding in a grass species.

PubMed

Atwater, Daniel Z; Callaway, Ragan M

2015-12-01

Plant diversity enhances many ecosystem processes, including productivity, but these effects have been studied almost exclusively at the taxonomic scale of species. We explore the effect of intraspecific diversity on the productivity of a widespread and dominant grassland species using accessions collected from populations throughout its range. We found that increasing population/ecotype diversity of Pseudoroegneria spicata increased productivity to a similar degree as that reported for species diversity. However, we did not find evidence that overyielding was related to either resource depletion or to pathogenic soil fungi, two causes of overyielding in species-diverse communities. Instead, larger accessions overyielded at low diversity at the expense of smaller accessions, and small accessions overyielded through complementarity at all levels of diversity. Furthermore, overyielding was stronger for accessions from mesic environments, suggesting that local adaptation might predictably influence how plants respond to increases in diversity. This suggests that mass-based competition or other cryptic accession-specific processes had complex but important effects on overyielding. Our results indicate that the effects of diversity within a species can be substantial but that overyielding by intraspecifically diverse populations may not be through the same processes thought to cause overyielding in species diverse communities.

Across species-pool aggregation alters grassland productivity and diversity.

PubMed

McKenna, Thomas P; Yurkonis, Kathryn A

2016-08-01

Plant performance is determined by the balance of intra- and interspecific neighbors within an individual's zone of influence. If individuals interact over smaller scales than the scales at which communities are measured, then altering neighborhood interactions may fundamentally affect community responses. These interactions can be altered by changing the number (species richness), abundances (species evenness), and positions (species pattern) of the resident plant species, and we aimed to test whether aggregating species at planting would alter effects of species richness and evenness on biomass production at a common scale of observation in grasslands. We varied plant species richness (2, 4, or 8 species and monocultures), evenness (0.64, 0.8, or 1.0), and pattern (planted randomly or aggregated in groups of four individuals) within 1 × 1 m plots established with transplants from a pool of 16 tallgrass prairie species and assessed plot-scale biomass production and diversity over the first three growing seasons. As expected, more species-rich plots produced more biomass by the end of the third growing season, an effect associated with a shift from selection to complementarity effects over time. Aggregating conspecifics at a 0.25-m scale marginally reduced biomass production across all treatments and increased diversity in the most even plots, but did not alter biodiversity effects or richness-productivity relationships. Results support the hypothesis that fine-scale species aggregation affects diversity by promoting species coexistence in this system. However, results indicate that inherent changes in species neighborhood relationships along grassland diversity gradients may only minimally affect community (meter) - scale responses among similarly designed biodiversity-ecosystem function studies. Given that species varied in their responses to local aggregation, it may be possible to use such species-specific results to spatially design larger-scale grassland

Species diversity of Trichoderma in Poland

USDA-ARS?s Scientific Manuscript database

Fifteen species of Trichoderma were identified from among 118 strains originating from different regions and ecological niches in Poland. This low number indicates low species diversity of Trichoderma in this Central European region. Using the ITS1-ITS2 regions, 64 strains were positively identified...

Tree species diversity promotes aboveground carbon storage through functional diversity and functional dominance.

PubMed

Mensah, Sylvanus; Veldtman, Ruan; Assogbadjo, Achille E; Glèlè Kakaï, Romain; Seifert, Thomas

2016-10-01

The relationship between biodiversity and ecosystem function has increasingly been debated as the cornerstone of the processes behind ecosystem services delivery. Experimental and natural field-based studies have come up with nonconsistent patterns of biodiversity-ecosystem function, supporting either niche complementarity or selection effects hypothesis. Here, we used aboveground carbon (AGC) storage as proxy for ecosystem function in a South African mistbelt forest, and analyzed its relationship with species diversity, through functional diversity and functional dominance. We hypothesized that (1) diversity influences AGC through functional diversity and functional dominance effects; and (2) effects of diversity on AGC would be greater for functional dominance than for functional diversity. Community weight mean (CWM) of functional traits (wood density, specific leaf area, and maximum plant height) were calculated to assess functional dominance (selection effects). As for functional diversity (complementarity effects), multitrait functional diversity indices were computed. The first hypothesis was tested using structural equation modeling. For the second hypothesis, effects of environmental variables such as slope and altitude were tested first, and separate linear mixed-effects models were fitted afterward for functional diversity, functional dominance, and both. Results showed that AGC varied significantly along the slope gradient, with lower values at steeper sites. Species diversity (richness) had positive relationship with AGC, even when slope effects were considered. As predicted, diversity effects on AGC were mediated through functional diversity and functional dominance, suggesting that both the niche complementarity and the selection effects are not exclusively affecting carbon storage. However, the effects were greater for functional diversity than for functional dominance. Furthermore, functional dominance effects were strongly transmitted by CWM of

Gastric colonisation with a restricted commensal microbiota replicates the promotion of neoplastic lesions by diverse intestinal microbiota in the Helicobacter pylori INS-GAS mouse model of gastric carcinogenesis

PubMed Central

Lertpiriyapong, Kvin; Whary, Mark T.; Muthupalani, Sureshkumar; Lofgren, Jennifer L.; Gamazon, Eric R.; Feng, Yan; Ge, Zhongming; Wang, Timothy C.; Fox, James G.

2014-01-01

Objectives Gastric colonisation with intestinal flora (IF) has been shown to promote Helicobacter pylori (Hp)-associated gastric cancer. However, it is unknown if the mechanism involves colonisation with specific or diverse microbiota secondary to gastric atrophy. Design Gastric colonisation with Altered Schaedler’s flora (ASF) and Hp were correlated with pathology, immune responses and mRNA expression for proinflammatory and cancer-related genes in germ-free (GF), Hp monoassociated (mHp), restricted ASF (rASF; 3 species), and specific pathogen-free (complex IF), hypergastrinemic INS-GAS mice 7 months postinfection. Results Male mice cocolonised with rASFHp or IFHp developed the most severe pathology. IFHp males had the highest inflammatory responses, and 40% developed invasive gastrointestinal intraepithelial neoplasia (GIN). Notably, rASFHp colonisation was highest in males and 23% developed invasive GIN with elevated expression of inflammatory biomarkers. Lesions were less severe in females and none developed GIN. Gastritis in male rASFHp mice was accompanied by decreased Clostridum species ASF356 and Bacteroides species ASF519 colonisation and an overgrowth of Lactobacillus murinus ASF361, supporting that inflammation-driven atrophy alters the gastric niche for GI commensals. Hp colonisation also elevated expression of IL-11 and cancer-related genes, Ptger4 and Tgf-β, further supporting that Hp infection accelerates gastric cancer development in INS-GAS mice. Conclusions rASFHp colonisation was sufficient for GIN development in males, and lower GIN incidence in females was associated with lower inflammatory responses and gastric commensal and Hp colonisation. Colonisation efficiency of commensals appears more important than microbial diversity and lessens the probability that specific gastrointestinal pathogens are contributing to cancer risk. PMID:23812323

Helicobacter pylori-induced gastric pathology: insights from in vivo and ex vivo models.

PubMed

Burkitt, Michael D; Duckworth, Carrie A; Williams, Jonathan M; Pritchard, D Mark

2017-02-01

Gastric colonization with Helicobacter pylori induces diverse human pathological conditions, including superficial gastritis, peptic ulcer disease, mucosa-associated lymphoid tissue (MALT) lymphoma, and gastric adenocarcinoma and its precursors. The treatment of these conditions often relies on the eradication of H. pylori, an intervention that is increasingly difficult to achieve and that does not prevent disease progression in some contexts. There is, therefore, a pressing need to develop new experimental models of H. pylori-associated gastric pathology to support novel drug development in this field. Here, we review the current status of in vivo and ex vivo models of gastric H. pylori colonization, and of Helicobacter-induced gastric pathology, focusing on models of gastric pathology induced by H. pylori, Helicobacter felis and Helicobacter suis in rodents and large animals. We also discuss the more recent development of gastric organoid cultures from murine and human gastric tissue, as well as from human pluripotent stem cells, and the outcomes of H. pylori infection in these systems. © 2017. Published by The Company of Biologists Ltd.

Helicobacter acinonychis: genetic and rodent infection studies of a Helicobacter pylori-like gastric pathogen of cheetahs and other big cats.

PubMed

Dailidiene, Daiva; Dailide, Giedrius; Ogura, Keiji; Zhang, Maojun; Mukhopadhyay, Asish K; Eaton, Kathryn A; Cattoli, Giovanni; Kusters, Johannes G; Berg, Douglas E

2004-01-01

Insights into bacterium-host interactions and genome evolution can emerge from comparisons among related species. Here we studied Helicobacter acinonychis (formerly H. acinonyx), a species closely related to the human gastric pathogen Helicobacter pylori. Two groups of strains were identified by randomly amplified polymorphic DNA fingerprinting and gene sequencing: one group from six cheetahs in a U.S. zoo and two lions in a European circus, and the other group from a tiger and a lion-tiger hybrid in the same circus. PCR and DNA sequencing showed that each strain lacked the cag pathogenicity island and contained a degenerate vacuolating cytotoxin (vacA) gene. Analyses of nine other genes (glmM, recA, hp519, glr, cysS, ppa, flaB, flaA, and atpA) revealed a approximately 2% base substitution difference, on average, between the two H. acinonychis groups and a approximately 8% difference between these genes and their homologs in H. pylori reference strains such as 26695. H. acinonychis derivatives that could chronically infect mice were selected and were found to be capable of persistent mixed infection with certain H. pylori strains. Several variants, due variously to recombination or new mutation, were found after 2 months of mixed infection. H. acinonychis ' modest genetic distance from H. pylori, its ability to infect mice, and its ability to coexist and recombine with certain H. pylori strains in vivo should be useful in studies of Helicobacter infection and virulence mechanisms and studies of genome evolution.

Stand structural diversity rather than species diversity enhances aboveground carbon storage in secondary subtropical forests in Eastern China

NASA Astrophysics Data System (ADS)

Ali, Arshad; Yan, En-Rong; Chen, Han Y. H.; Chang, Scott X.; Zhao, Yan-Tao; Yang, Xiao-Dong; Xu, Ming-Shan

2016-08-01

Stand structural diversity, typically characterized by variances in tree diameter at breast height (DBH) and total height, plays a critical role in influencing aboveground carbon (C) storage. However, few studies have considered the multivariate relationships of aboveground C storage with stand age, stand structural diversity, and species diversity in natural forests. In this study, aboveground C storage, stand age, tree species, DBH and height diversity indices, were determined across 80 subtropical forest plots in Eastern China. We employed structural equation modelling (SEM) to test for the direct and indirect effects of stand structural diversity, species diversity, and stand age on aboveground C storage. The three final SEMs with different directions for the path between species diversity and stand structural diversity had a similar goodness of fit to the data. They accounted for 82 % of the variation in aboveground C storage, 55-59 % of the variation in stand structural diversity, and 0.1 to 9 % of the variation in species diversity. Stand age demonstrated strong positive total effects, including a positive direct effect (β = 0.41), and a positive indirect effect via stand structural diversity (β = 0.41) on aboveground C storage. Stand structural diversity had a positive direct effect on aboveground C storage (β = 0.56), whereas there was little total effect of species diversity as it had a negative direct association with, but had a positive indirect effect, via stand structural diversity, on aboveground C storage. The negligible total effect of species diversity on aboveground C storage in the forests under study may have been attributable to competitive exclusion with high aboveground biomass, or a historical logging preference for productive species. Our analyses suggested that stand structural diversity was a major determinant for variations in aboveground C storage in the secondary subtropical forests in Eastern China. Hence, maintaining tree DBH and

Genetic calibration of species diversity among North America's freshwater fishes.

PubMed

April, Julien; Mayden, Richard L; Hanner, Robert H; Bernatchez, Louis

2011-06-28

Freshwater ecosystems are being heavily exploited and degraded by human activities all over the world, including in North America, where fishes and fisheries are strongly affected. Despite centuries of taxonomic inquiry, problems inherent to species identification continue to hamper the conservation of North American freshwater fishes. Indeed, nearly 10% of species diversity is thought to remain undescribed. To provide an independent calibration of taxonomic uncertainty and to establish a more accessible molecular identification key for its application, we generated a standard reference library of mtDNA sequences (DNA barcodes) derived from expert-identified museum specimens for 752 North American freshwater fish species. This study demonstrates that 90% of known species can be delineated using barcodes. Moreover, it reveals numerous genetic discontinuities indicative of independently evolving lineages within described species, which points to the presence of morphologically cryptic diversity. From the 752 species analyzed, our survey flagged 138 named species that represent as many as 347 candidate species, which suggests a 28% increase in species diversity. In contrast, several species of parasitic and nonparasitic lampreys lack such discontinuity and may represent alternative life history strategies within single species. Therefore, it appears that the current North American freshwater fish taxonomy at the species level significantly conceals diversity in some groups, although artificially creating diversity in others. In addition to providing an easily accessible digital identification system, this study identifies 151 fish species for which taxonomic revision is required.

Genetic calibration of species diversity among North America's freshwater fishes

PubMed Central

April, Julien; Mayden, Richard L.; Hanner, Robert H.; Bernatchez, Louis

2011-01-01

Freshwater ecosystems are being heavily exploited and degraded by human activities all over the world, including in North America, where fishes and fisheries are strongly affected. Despite centuries of taxonomic inquiry, problems inherent to species identification continue to hamper the conservation of North American freshwater fishes. Indeed, nearly 10% of species diversity is thought to remain undescribed. To provide an independent calibration of taxonomic uncertainty and to establish a more accessible molecular identification key for its application, we generated a standard reference library of mtDNA sequences (DNA barcodes) derived from expert-identified museum specimens for 752 North American freshwater fish species. This study demonstrates that 90% of known species can be delineated using barcodes. Moreover, it reveals numerous genetic discontinuities indicative of independently evolving lineages within described species, which points to the presence of morphologically cryptic diversity. From the 752 species analyzed, our survey flagged 138 named species that represent as many as 347 candidate species, which suggests a 28% increase in species diversity. In contrast, several species of parasitic and nonparasitic lampreys lack such discontinuity and may represent alternative life history strategies within single species. Therefore, it appears that the current North American freshwater fish taxonomy at the species level significantly conceals diversity in some groups, although artificially creating diversity in others. In addition to providing an easily accessible digital identification system, this study identifies 151 fish species for which taxonomic revision is required. PMID:21670289

The relationship between species diversity and genetic structure in the rare Picea chihuahuana tree species community, Mexico.

PubMed

Simental-Rodríguez, Sergio Leonel; Quiñones-Pérez, Carmen Zulema; Moya, Daniel; Hernández-Tecles, Enrique; López-Sánchez, Carlos Antonio; Wehenkel, Christian

2014-01-01

Species diversity and genetic diversity, the most basic elements of biodiversity, have long been treated as separate topics, although populations evolve within a community context. Recent studies on community genetics and ecology have suggested that genetic diversity is not completely independent of species diversity. The Mexican Picea chihuahuana Martínez is an endemic species listed as "Endangered" on the Red List. Forty populations of Chihuahua spruce have been identified. This species is often associated with tree species of eight genera in gallery forests. This rare Picea chihuahuana tree community covers an area no more than 300 ha and has been subject of several studies involving different topics such as ecology, genetic structure and climate change. The overall aim of these studies was to obtain a dataset for developing management tools to help decision makers implement preservation and conservation strategies. However, this unique forest tree community may also represent an excellent subject for helping us to understand the interplay between ecological and evolutionary processes in determining community structure and dynamics. The AFLP technique and species composition data were used together to test the hypothesis that species diversity is related to the adaptive genetic structure of some dominant tree species (Picea chihuahuana, Pinus strobiformis, Pseudotsuga menziesii and Populus tremuloides) of the Picea chihuahuana tree community at fourteen locations. The Hill numbers were used as a diversity measure. The results revealed a significant correlation between tree species diversity and genetic structure in Populus tremuloides. Because the relationship between the two levels of diversity was found to be positive for the putative adaptive AFLP detected, genetic and species structures of the tree community were possibly simultaneously adapted to a combination of ecological or environmental factors. The present findings indicate that interactions between

Region effects influence local tree species diversity.

PubMed

Ricklefs, Robert E; He, Fangliang

2016-01-19

Global patterns of biodiversity reflect both regional and local processes, but the relative importance of local ecological limits to species coexistence, as influenced by the physical environment, in contrast to regional processes including species production, dispersal, and extinction, is poorly understood. Failure to distinguish regional influences from local effects has been due, in part, to sampling limitations at small scales, environmental heterogeneity within local or regional samples, and incomplete geographic sampling of species. Here, we use a global dataset comprising 47 forest plots to demonstrate significant region effects on diversity, beyond the influence of local climate, which together explain more than 92% of the global variation in local forest tree species richness. Significant region effects imply that large-scale processes shaping the regional diversity of forest trees exert influence down to the local scale, where they interact with local processes to determine the number of coexisting species.

Rapid evolution of hosts begets species diversity at the cost of intraspecific diversity

PubMed Central

Frickel, Jens; Theodosiou, Loukas

2017-01-01

Ecosystems are complex food webs in which multiple species interact and ecological and evolutionary processes continuously shape populations and communities. Previous studies on eco-evolutionary dynamics have shown that the presence of intraspecific diversity affects community structure and function, and that eco-evolutionary feedback dynamics can be an important driver for its maintenance. Within communities, feedbacks are, however, often indirect, and they can feed back over many generations. Here, we studied eco-evolutionary feedbacks in evolving communities over many generations and compared two-species systems (virus–host and prey–predator) with a more complex three-species system (virus–host–predator). Both indirect density- and trait-mediated effects drove the dynamics in the complex system, where host–virus coevolution facilitated coexistence of predator and virus, and where coexistence, in return, lowered intraspecific diversity of the host population. Furthermore, ecological and evolutionary dynamics were significantly altered in the three-species system compared with the two-species systems. We found that the predator slowed host–virus coevolution in the complex system and that the virus’ effect on the overall population dynamics was negligible when the three species coexisted. Overall, we show that a detailed understanding of the mechanism driving eco-evolutionary feedback dynamics is necessary for explaining trait and species diversity in communities, even in communities with only three species. PMID:28973943

Rapid evolution of hosts begets species diversity at the cost of intraspecific diversity.

PubMed

Frickel, Jens; Theodosiou, Loukas; Becks, Lutz

2017-10-17

Ecosystems are complex food webs in which multiple species interact and ecological and evolutionary processes continuously shape populations and communities. Previous studies on eco-evolutionary dynamics have shown that the presence of intraspecific diversity affects community structure and function, and that eco-evolutionary feedback dynamics can be an important driver for its maintenance. Within communities, feedbacks are, however, often indirect, and they can feed back over many generations. Here, we studied eco-evolutionary feedbacks in evolving communities over many generations and compared two-species systems (virus-host and prey-predator) with a more complex three-species system (virus-host-predator). Both indirect density- and trait-mediated effects drove the dynamics in the complex system, where host-virus coevolution facilitated coexistence of predator and virus, and where coexistence, in return, lowered intraspecific diversity of the host population. Furthermore, ecological and evolutionary dynamics were significantly altered in the three-species system compared with the two-species systems. We found that the predator slowed host-virus coevolution in the complex system and that the virus' effect on the overall population dynamics was negligible when the three species coexisted. Overall, we show that a detailed understanding of the mechanism driving eco-evolutionary feedback dynamics is necessary for explaining trait and species diversity in communities, even in communities with only three species.

Multifaceted diversity-area relationships reveal global hotspots of mammalian species, trait and lineage diversity.

PubMed

Mazel, Florent; Guilhaumon, François; Mouquet, Nicolas; Devictor, Vincent; Gravel, Dominique; Renaud, Julien; Cianciaruso, Marcus Vinicius; Loyola, Rafael Dias; Diniz-Filho, José Alexandre Felizola; Mouillot, David; Thuiller, Wilfried

2014-08-01

To define biome-scale hotspots of phylogenetic and functional mammalian biodiversity (PD and FD, respectively) and compare them to 'classical' hotspots based on species richness (SR) only. Global. SR, PD & FD were computed for 782 terrestrial ecoregions using distribution ranges of 4616 mammalian species. We used a set of comprehensive diversity indices unified by a recent framework that incorporates the species relative coverage in each ecoregion. We build large-scale multifaceted diversity-area relationships to rank ecoregions according to their levels of biodiversity while accounting for the effect of area on each diversity facet. Finally we defined hotspots as the top-ranked ecoregions. While ignoring species relative coverage led to a relative good congruence between biome top ranked SR, PD and FD hotspots, ecoregions harboring a rich and abundantly represented evolutionary history and functional diversity did not match with top ranked ecoregions defined by species richness. More importantly PD and FD hotspots showed important spatial mismatches. We also found that FD and PD generally reached their maximum values faster than species richness as a function of area. The fact that PD/FD reach faster their maximal value than SR may suggest that the two former facets might be less vulnerable to habitat loss than the latter. While this point is expected, it is the first time that it is quantified at global scale and should have important consequences in conservation. Incorporating species relative coverage into the delineation of multifaceted hotspots of diversity lead to weak congruence between SR, PD and FD hotspots. This means that maximizing species number may fail at preserving those nodes (in the phylogenetic or functional tree) that are relatively abundant in the ecoregion. As a consequence it may be of prime importance to adopt a multifaceted biodiversity perspective to inform conservation strategies at global scale.

Multifaceted diversity-area relationships reveal global hotspots of mammalian species, trait and lineage diversity

PubMed Central

Mazel, Florent; Guilhaumon, François; Mouquet, Nicolas; Devictor, Vincent; Gravel, Dominique; Renaud, Julien; Cianciaruso, Marcus Vinicius; Loyola, Rafael Dias; Diniz-Filho, José Alexandre Felizola; Mouillot, David; Thuiller, Wilfried

2014-01-01

Aim To define biome-scale hotspots of phylogenetic and functional mammalian biodiversity (PD and FD, respectively) and compare them to ‘classical’ hotspots based on species richness (SR) only. Location Global Methods SR, PD & FD were computed for 782 terrestrial ecoregions using distribution ranges of 4616 mammalian species. We used a set of comprehensive diversity indices unified by a recent framework that incorporates the species relative coverage in each ecoregion. We build large-scale multifaceted diversity-area relationships to rank ecoregions according to their levels of biodiversity while accounting for the effect of area on each diversity facet. Finally we defined hotspots as the top-ranked ecoregions. Results While ignoring species relative coverage led to a relative good congruence between biome top ranked SR, PD and FD hotspots, ecoregions harboring a rich and abundantly represented evolutionary history and functional diversity did not match with top ranked ecoregions defined by species richness. More importantly PD and FD hotspots showed important spatial mismatches. We also found that FD and PD generally reached their maximum values faster than species richness as a function of area. Main conclusions The fact that PD/FD reach faster their maximal value than SR may suggest that the two former facets might be less vulnerable to habitat loss than the latter. While this point is expected, it is the first time that it is quantified at global scale and should have important consequences in conservation. Incorporating species relative coverage into the delineation of multifaceted hotspots of diversity lead to weak congruence between SR, PD and FD hotspots. This means that maximizing species number may fail at preserving those nodes (in the phylogenetic or functional tree) that are relatively abundant in the ecoregion. As a consequence it may be of prime importance to adopt a multifaceted biodiversity perspective to inform conservation strategies at global

Species replacement dominates megabenthos beta diversity in a remote seamount setting.

PubMed

Victorero, Lissette; Robert, Katleen; Robinson, Laura F; Taylor, Michelle L; Huvenne, Veerle A I

2018-03-07

Seamounts are proposed to be hotspots of deep-sea biodiversity, a pattern potentially arising from increased productivity in a heterogeneous landscape leading to either high species co-existence or species turnover (beta diversity). However, studies on individual seamounts remain rare, hindering our understanding of the underlying causes of local changes in beta diversity. Here, we investigated processes behind beta diversity using ROV video, coupled with oceanographic and quantitative terrain parameters, over a depth gradient in Annan Seamount, Equatorial Atlantic. By applying recently developed beta diversity analyses, we identified ecologically unique sites and distinguished between two beta diversity processes: species replacement and changes in species richness. The total beta diversity was high with an index of 0.92 out of 1 and was dominated by species replacement (68%). Species replacement was affected by depth-related variables, including temperature and water mass in addition to the aspect and local elevation of the seabed. In contrast, changes in species richness component were affected only by the water mass. Water mass, along with substrate also affected differences in species abundance. This study identified, for the first time on seamount megabenthos, the different beta diversity components and drivers, which can contribute towards understanding and protecting regional deep-sea biodiversity.

Comparison of Helicobacter spp. in Cheetahs (Acinonyx jubatus) with and without gastritis.

PubMed

Terio, K A; Munson, L; Marker, L; Aldridge, B M; Solnick, J V

2005-01-01

Chronic gastritis causes significant morbidity and mortality in captive cheetahs but is rare in wild cheetahs despite colonization by abundant spiral bacteria. This research aimed to identify the Helicobacter species that were associated with gastritis in captive cheetahs but are apparently commensal in wild cheetahs. Helicobacter species were characterized by PCR amplification and sequencing of the 16S rRNA, urease, and cagA genes and by transmission electron microscopy of frozen or formalin-fixed paraffin-embedded gastric samples from 33 cheetahs infected with Helicobacter organisms (10 wild without gastritis and 23 captive with gastritis). Samples were screened for mixed infections by denaturant gel gradient electrophoresis of the 16S rRNA gene and by transmission electron microscopy. There was no association between Helicobacter infection and the presence or severity of gastritis. Eight cheetahs had 16S rRNA sequences that were most similar (98 to 99%) to H. pylori. Twenty-five cheetahs had sequences that were most similar (97 to 99%) to "H. heilmannii" or H. felis. No cheetahs had mixed infections. The ultrastructural morphology of all bacteria was most consistent with "H. heilmannii," even when 16S rRNA sequences were H. pylori-like. The urease gene from H. pylori-like bacteria could not be amplified with primers for either "H. heilmannii" or H. pylori urease, suggesting that this bacteria is neither H. pylori nor "H. heilmannii." The cagA gene was not identified in any case. These findings question a direct role for Helicobacter infection in the pathogenesis of gastritis and support the premise that host factors account for the differences in disease between captive and wild cheetah populations.

High levels of cryptic species diversity uncovered in Amazonian frogs

PubMed Central

Funk, W. Chris; Caminer, Marcel; Ron, Santiago R.

2012-01-01

One of the greatest challenges for biodiversity conservation is the poor understanding of species diversity. Molecular methods have dramatically improved our ability to uncover cryptic species, but the magnitude of cryptic diversity remains unknown, particularly in diverse tropical regions such as the Amazon Basin. Uncovering cryptic diversity in amphibians is particularly pressing because amphibians are going extinct globally at an alarming rate. Here, we use an integrative analysis of two independent Amazonian frog clades, Engystomops toadlets and Hypsiboas treefrogs, to test whether species richness is underestimated and, if so, by how much. We sampled intensively in six countries with a focus in Ecuador (Engystomops: 252 individuals from 36 localities; Hypsiboas: 208 individuals from 65 localities) and combined mitochondrial DNA, nuclear DNA, morphological, and bioacoustic data to detect cryptic species. We found that in both clades, species richness was severely underestimated, with more undescribed species than described species. In Engystomops, the two currently recognized species are actually five to seven species (a 150–250% increase in species richness); in Hypsiboas, two recognized species represent six to nine species (a 200–350% increase). Our results suggest that Amazonian frog biodiversity is much more severely underestimated than previously thought. PMID:22130600

Contrasting species and functional beta diversity in montane ant assemblages.

PubMed

Bishop, Tom R; Robertson, Mark P; van Rensburg, Berndt J; Parr, Catherine L

2015-09-01

Beta diversity describes the variation in species composition between sites and can be used to infer why different species occupy different parts of the globe. It can be viewed in a number of ways. First, it can be partitioned into two distinct patterns: turnover and nestedness. Second, it can be investigated from either a species identity or a functional-trait point of view. We aim to document for the first time how these two aspects of beta diversity vary in response to a large environmental gradient. Maloti-Drakensberg Mountains, southern Africa. We sampled ant assemblages along an extensive elevational gradient (900-3000 m a.s.l.) twice yearly for 7 years, and collected functional-trait information related to the species' dietary and habitat-structure preferences. We used recently developed methods to partition species and functional beta diversity into their turnover and nestedness components. A series of null models were used to test whether the observed beta diversity patterns differed from random expectations. Species beta diversity was driven by turnover, but functional beta diversity was composed of both turnover and nestedness patterns at different parts of the gradient. Null models revealed that deterministic processes were likely to be responsible for the species patterns but that the functional changes were indistinguishable from stochasticity. Different ant species are found with increasing elevation, but they tend to represent an increasingly nested subset of the available functional strategies. This finding is unique and narrows down the list of possible factors that control ant existence across elevation. We conclude that diet and habitat preferences have little role in structuring ant assemblages in montane environments and that some other factor must be driving the non-random patterns of species turnover. This finding also highlights the importance of distinguishing between different kinds of beta diversity.

Diverse vacA allelic types of Helicobacter pylori in Korea and clinical correlation.

PubMed

Choe, Yon Ho; Kim, Pum Soo; Lee, Don Haeng; Kim, Hyung Kil; Kim, Young Soo; Shin, Yong Woon; Hwang, Tae Sook; Kim, Hyeon Joo; Song, Sun Uk; Choi, Mi Sook

2002-06-01

Helicobacter pylori has a diversity of vacA allelic types. The purpose of this study was to correlate the vacA status and the clinical outcome. After constructing specific primers for the vacA signal sequence, H. pylori-positive antral biopsy specimens were examined for the vacA status in 25 gastric ulcers, 31 duodenal ulcers, 22 gastric cancers, 42 chronic gastritis, and 8 gastroduodenal ulcers. The relationship between the vacA allele and the clinical disease was examined. The vacA genotype s1c/m1 is predominant in Korea (71/128, 55.5%). Other strains including s1b or s2 were not found in this study. s1c/m1 was more prominent in duodenal ulcers, than in gastric ulcers (p=0.041) and cancer (p=0.029). Seven out of 8 patients with gastric and coexistent duodenal ulcers had the s1c/m1 allele. No statistical differences in the positive rates of the s1a/m1, s1a/m2, and s1c/m2 alleles among the disease groups were found. In conclusion, s1c/m1 is the main vacA allele in Korea and it is particularly associated with duodenal ulcers.

Novel Helicobacter species H.japonicum isolated from laboratory mice from Japan induces typhlocolitis and lower bowel carcinoma in C57BL/129 IL10−/− mice

PubMed Central

Shen, Zeli; Feng, Yan; Muthupalani, Sureshkumar; Sheh, Alexander; Cheaney, Lenzie E.; Kaufman, Christian A.; Gong, Guanyu; Paster, Bruce J.; Fox, James G.

2016-01-01

A novel Helicobacter species Helicobacter japonicum was isolated from the stomach and intestines of clinically normal mice received from three institutes from Japan. The novel Helicobacter sp. was microaerobic, grew at 37°C and 42°C, was catalase and oxidase positive, but urease negative. It is most closely related to the 16S rRNA gene of H.muridarum (98.6%); to the 23S rRNA gene of H.hepaticus (97.9%); to the hsp60 gene of H.typhlonius (87%). The novel Helicobacter sp. has in vitro cytolethal distending toxin (CDT) activity; its cdtB gene sequence has 83.8% identity with that of H.hepaticus. The whole genome sequence of H.japonicum MIT 01-6451 has a 2.06-Mb genome length with a 37.5% G + C content. When the organism was inoculated into C57BL/129 IL10−/− mice, it was cultured from the stomach, colon and cecum of infected mice at 6 and 10 weeks post-infection. The cecum had the highest H.japonicum colonization levels by quantitative PCR. The histopathology of the lower bowel was characterized by moderate to severe inflammation, mild edema, epithelial defects, mild to severe hyperplasia, dysplasia and carcinoma. Inflammatory cytokines IFNγ, TNFα and IL17a, as well as iNOS were significantly upregulated in the cecal tissue of infected mice. These results demonstrate that the novel H.japonicum can induce inflammatory bowel disease and carcinoma in IL10−/− mice and highlights the importance of identifying novel Helicobacter spp. especially when they are introduced from outside mouse colonies from different geographic locations. PMID:27655833

Avian Species and Functional Diversity in Agricultural Landscapes: Does Landscape Heterogeneity Matter?

PubMed

Lee, Myung-Bok; Martin, James A

2017-01-01

While the positive relationship between avian diversity and habitat heterogeneity is widely accepted, it is primarily based on observed species richness without accounting for imperfect detection. Other facets of diversity such as functional diversity are also rarely explored. We investigated the avian diversity-landscape heterogeneity relationship in agricultural landscapes by considering two aspects of diversity: taxonomic diversity (species richness) estimated from a multi-species dynamic occupancy model, and functional diversity (functional evenness [FEve] and divergence [FDiv]) based on traits of occurring species. We also assessed how agricultural lands enrolled in a conservation program managed on behalf of declining early successional bird species (hereafter CP38 fields, an agri-environment scheme) influenced avian diversity. We analyzed breeding bird data collected at CP38 fields in Mississippi, USA, during 2010-2012, and two principal components of environmental variables: a gradient of heterogeneity (Shannon's landscape diversity index) and of the amount of CP38 fields (percent cover of CP38 fields; CP38). FEve did not show significant responses to environmental variables, whereas FDiv responded positively to heterogeneity and negatively to CP38. However, most FDiv values did not significantly differ from random expectations along an environmental gradient. When there was a significant difference, FDiv was lower than that expected. Unlike functional diversity, species richness showed a clear pattern. Species richness increased with increasing landscape heterogeneity but decreased with increasing amounts of CP38 fields. Only one species responded negatively to heterogeneity and positively to CP38. Our results suggest that the relationships between avian diversity and landscape heterogeneity may vary depending on the aspect of diversity considered: strong positive effects of heterogeneity on taxonomic diversity, but weakly positive or non

The effect of organic farming systems on species diversity

NASA Astrophysics Data System (ADS)

Leksono, Amin Setyo

2017-11-01

Organic farming systems have been well known to support the diversity of a wide range of taxa, including microorganisms, arable flora, invertebrates, birds, and mammals, which benefit from organic management leading to increases in abundance and/or species richness. The objective of this paper is to review the effect of organic farming on species diversity reported in several articles and compare this with the current study in Gondanglegi, Malang. A review of several studies showed that organic farming systems have been reported to increase species diversity, including that of mammals, birds, arthropods, vascular plants and arbuscular mycorrhizal fungi. The researchers about arthropod groups consisted of carabid beetles, butterflies, wasps, predators, and bees. Agricultural landscape, habitat type, farming system, landscape composition and connectivity all contribute to explaining species biodiversity and richness. Moreover, based on current and relevant studies, the results showed that the application of refugia blocks has increased arthropod diversity and composition.

Sown species richness and realized diversity can influence functioning of plant communities differently.

PubMed

Rychtecká, Terezie; Lanta, Vojtěch; Weiterová, Iva; Lepš, Jan

2014-08-01

Biodiversity-ecosystem functioning experiments (BEF) typically manipulate sown species richness and composition of experimental communities to study ecosystem functioning as a response to changes in diversity. If sown species richness is taken as a measure of diversity and aboveground biomass production as a measure of community functioning, then this relationship is usually found to be positive. The sown species richness can be considered the equivalent of a local species pool in natural communities. However, in addition to species richness, realized diversity is also an important community diversity component. Realized diversity is affected by environmental filtering and biotic interactions operating within a community. As both sown species richness and the realized diversity in BEF studies (as well as local species pool vs observed realized richness in natural communities) can differ markedly, so can their effects on the community functioning. We tested this assumption using two data sets: data from a short-term pot experiment and data from the long-term Jena biodiversity plot experiment. We considered three possible predictors of community functioning (aboveground biomass production): sown species richness, realized diversity (defined as inverse of Simpson dominance index), and survivor species richness. Sown species richness affected biomass production positively in all cases. Realized diversity as well as survivor species richness had positive effects on biomass in approximately half of cases. When realized diversity or survivor species richness was tested together with sown species richness, their partial effects were none or negative. Our results suggest that we can expect positive diversity-productivity relationship when the local species pool size is the decisive factor determining realized observed diversity; in other cases, the shape of the diversity-functioning relationship may be quite opposite.

Detection of Helicobacter and Campylobacter spp. from the aquatic environment of marine mammals.

PubMed

Goldman, C G; Matteo, M J; Loureiro, J D; Degrossi, J; Teves, S; Heredia, S Rodriguez; Alvarez, K; González, A Beltrán; Catalano, M; Boccio, J; Cremaschi, G; Solnick, J V; Zubillaga, M B

2009-01-13

The mechanism by which Helicobacter species are transmitted remains unclear. To examine the possible role of environmental transmission in marine mammals, we sought the presence of Helicobacter spp. and non-Helicobacter bacteria within the order Campylobacterales in water from the aquatic environment of marine mammals, and in fish otoliths regurgitated by dolphins. Water was collected from six pools, two inhabited by dolphins and four inhabited by seals. Regurgitated otoliths were collected from the bottom of dolphins' pools. Samples were evaluated by culture, PCR and DNA sequence analysis. Sequences from dolphins' water and from regurgitated otoliths clustered with 99.8-100% homology with sequences from gastric fluids, dental plaque and saliva from dolphins living in those pools, and with 99.5% homology with H. cetorum. Sequences from seals' water clustered with 99.5% homology with a sequence amplified from a Northern sea lion (AY203900). Control PCR on source water for the pools and from otoliths dissected from feeder fish were negative. The findings of Helicobacter spp. DNA in the aquatic environment suggests that contaminated water from regurgitated fish otoliths and perhaps other tissues may play a role in Helicobacter transmission among marine mammals.

Rare species support vulnerable functions in high-diversity ecosystems.

PubMed

Mouillot, David; Bellwood, David R; Baraloto, Christopher; Chave, Jerome; Galzin, Rene; Harmelin-Vivien, Mireille; Kulbicki, Michel; Lavergne, Sebastien; Lavorel, Sandra; Mouquet, Nicolas; Paine, C E Timothy; Renaud, Julien; Thuiller, Wilfried

2013-01-01

Around the world, the human-induced collapses of populations and species have triggered a sixth mass extinction crisis, with rare species often being the first to disappear. Although the role of species diversity in the maintenance of ecosystem processes has been widely investigated, the role of rare species remains controversial. A critical issue is whether common species insure against the loss of functions supported by rare species. This issue is even more critical in species-rich ecosystems where high functional redundancy among species is likely and where it is thus often assumed that ecosystem functioning is buffered against species loss. Here, using extensive datasets of species occurrences and functional traits from three highly diverse ecosystems (846 coral reef fishes, 2,979 alpine plants, and 662 tropical trees), we demonstrate that the most distinct combinations of traits are supported predominantly by rare species both in terms of local abundance and regional occupancy. Moreover, species that have low functional redundancy and are likely to support the most vulnerable functions, with no other species carrying similar combinations of traits, are rarer than expected by chance in all three ecosystems. For instance, 63% and 98% of fish species that are likely to support highly vulnerable functions in coral reef ecosystems are locally and regionally rare, respectively. For alpine plants, 32% and 89% of such species are locally and regionally rare, respectively. Remarkably, 47% of fish species and 55% of tropical tree species that are likely to support highly vulnerable functions have only one individual per sample on average. Our results emphasize the importance of rare species conservation, even in highly diverse ecosystems, which are thought to exhibit high functional redundancy. Rare species offer more than aesthetic, cultural, or taxonomic diversity value; they disproportionately increase the potential breadth of functions provided by ecosystems across

Dynamics of Tree Species Diversity in Unlogged and Selectively Logged Malaysian Forests.

PubMed

Shima, Ken; Yamada, Toshihiro; Okuda, Toshinori; Fletcher, Christine; Kassim, Abdul Rahman

2018-01-18

Selective logging that is commonly conducted in tropical forests may change tree species diversity. In rarely disturbed tropical forests, locally rare species exhibit higher survival rates. If this non-random process occurs in a logged forest, the forest will rapidly recover its tree species diversity. Here we determined whether a forest in the Pasoh Forest Reserve, Malaysia, which was selectively logged 40 years ago, recovered its original species diversity (species richness and composition). To explore this, we compared the dynamics of secies diversity between unlogged forest plot (18.6 ha) and logged forest plot (5.4 ha). We found that 40 years are not sufficient to recover species diversity after logging. Unlike unlogged forests, tree deaths and recruitments did not contribute to increased diversity in the selectively logged forests. Our results predict that selectively logged forests require a longer time at least than our observing period (40 years) to regain their diversity.

Persistent infection of rhesus monkeys with 'Helicobacter macacae' and its isolation from an animal with intestinal adenocarcinoma.

PubMed

Marini, Robert P; Muthupalani, Sureshkumar; Shen, Zeli; Buckley, Ellen M; Alvarado, Cynthia; Taylor, Nancy S; Dewhirst, Floyd E; Whary, Mark T; Patterson, Mary M; Fox, James G

2010-08-01

A novel helicobacter, 'Helicobacter macacae', was previously isolated from a colony of rhesus and cynomolgus monkeys in which diarrhoea from chronic idiopathic colitis was enzootic. A survey performed in a second colony of rhesus monkeys without a history of chronic diarrhoea determined that 57 % were faecal-culture positive for Helicobacter species. Ten years after the survey, one of the animals from which 'H. macacae' had been isolated, a 23-year-old, intact male rhesus monkey (Macaca mulatta), presented with partial inappetence and progressive weight loss. Subsequent evaluation of the monkey revealed anaemia, hypoproteinaemia, hypoalbuminaemia and a palpable abdominal mass. Contrast radiography suggested partial intestinal obstruction. The animal was euthanized and a diagnosis was made of intestinal adenocarcinoma of the ileocaecocolic junction with metastasis to regional lymph nodes and liver. Microaerobic culture of caecal tissue yielded a helicobacter organism identified as 'H. macacae' by 16S rRNA gene sequencing - the same species of bacteria isolated 10 years previously. The liver, small intestine and colon were also positive by PCR for Helicobacter species. Intestinal adenocarcinoma is the most common malignancy of aged macaques. Faeces or caecal tissue from five out of five monkeys that remained from the original cohort and that were colonized with 'H. macacae' in the initial survey were positive for the organism. The apparent persistence of 'H. macacae' in these animals, the isolation of the bacterium from animals with colitis and the recognition of the importance of inflammation in carcinogenesis raise the possibility of an aetiological role in the genesis of intestinal adenocarcinoma in aged rhesus monkeys.

Comparison of Helicobacter spp. in Cheetahs (Acinonyx jubatus) with and without Gastritis

PubMed Central

Terio, K. A.; Munson, L.; Marker, L.; Aldridge, B. M.; Solnick, J. V.

2005-01-01

Chronic gastritis causes significant morbidity and mortality in captive cheetahs but is rare in wild cheetahs despite colonization by abundant spiral bacteria. This research aimed to identify the Helicobacter species that were associated with gastritis in captive cheetahs but are apparently commensal in wild cheetahs. Helicobacter species were characterized by PCR amplification and sequencing of the 16S rRNA, urease, and cagA genes and by transmission electron microscopy of frozen or formalin-fixed paraffin-embedded gastric samples from 33 cheetahs infected with Helicobacter organisms (10 wild without gastritis and 23 captive with gastritis). Samples were screened for mixed infections by denaturant gel gradient electrophoresis of the 16S rRNA gene and by transmission electron microscopy. There was no association between Helicobacter infection and the presence or severity of gastritis. Eight cheetahs had 16S rRNA sequences that were most similar (98 to 99%) to H. pylori. Twenty-five cheetahs had sequences that were most similar (97 to 99%) to “H. heilmannii” or H. felis. No cheetahs had mixed infections. The ultrastructural morphology of all bacteria was most consistent with “H. heilmannii,” even when 16S rRNA sequences were H. pylori-like. The urease gene from H. pylori-like bacteria could not be amplified with primers for either “H. heilmannii” or H. pylori urease, suggesting that this bacteria is neither H. pylori nor “H. heilmannii.” The cagA gene was not identified in any case. These findings question a direct role for Helicobacter infection in the pathogenesis of gastritis and support the premise that host factors account for the differences in disease between captive and wild cheetah populations. PMID:15634976

Avian Species and Functional Diversity in Agricultural Landscapes: Does Landscape Heterogeneity Matter?

PubMed Central

2017-01-01

While the positive relationship between avian diversity and habitat heterogeneity is widely accepted, it is primarily based on observed species richness without accounting for imperfect detection. Other facets of diversity such as functional diversity are also rarely explored. We investigated the avian diversity-landscape heterogeneity relationship in agricultural landscapes by considering two aspects of diversity: taxonomic diversity (species richness) estimated from a multi-species dynamic occupancy model, and functional diversity (functional evenness [FEve] and divergence [FDiv]) based on traits of occurring species. We also assessed how agricultural lands enrolled in a conservation program managed on behalf of declining early successional bird species (hereafter CP38 fields, an agri-environment scheme) influenced avian diversity. We analyzed breeding bird data collected at CP38 fields in Mississippi, USA, during 2010–2012, and two principal components of environmental variables: a gradient of heterogeneity (Shannon’s landscape diversity index) and of the amount of CP38 fields (percent cover of CP38 fields; CP38). FEve did not show significant responses to environmental variables, whereas FDiv responded positively to heterogeneity and negatively to CP38. However, most FDiv values did not significantly differ from random expectations along an environmental gradient. When there was a significant difference, FDiv was lower than that expected. Unlike functional diversity, species richness showed a clear pattern. Species richness increased with increasing landscape heterogeneity but decreased with increasing amounts of CP38 fields. Only one species responded negatively to heterogeneity and positively to CP38. Our results suggest that the relationships between avian diversity and landscape heterogeneity may vary depending on the aspect of diversity considered: strong positive effects of heterogeneity on taxonomic diversity, but weakly positive or non

The significance of developmental robustness for species diversity.

PubMed

Melzer, Rainer; Theißen, Günter

2016-04-01

The origin of new species and of new forms is one of the fundamental characteristics of evolution. However, the mechanisms that govern the diversity and disparity of lineages remain poorly understood. Particularly unclear are the reasons why some taxa are vastly more species-rich than others and the manner in which species diversity and morphological disparity are interrelated. Evolutionary innovations and ecological opportunities are usually cited as among the major factors promoting the evolution of species diversity. In many cases it is likely that these factors are positively reinforcing, with evolutionary innovations creating ecological opportunities that in turn foster the origin of new innovations. However, we propose that a third factor, developmental robustness, is very often essential for this reinforcement to be effective. Evolutionary innovations need to be stably and robustly integrated into the developmental genetic programme of an organism to be a suitable substrate for selection to 'explore' ecological opportunities and morphological 'design' space (morphospace). In particular, we propose that developmental robustness of the bauplan is often a prerequisite for the exploration of morphospace and to enable the evolution of further novelties built upon this bauplan Thus, while robustness may reduce the morphological disparity at one level, it may be the basis for increased morphological disparity and for evolutionary innovations at another level, thus fostering species diversity. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Are Tree Species Diversity and Genotypic Diversity Effects on Insect Herbivores Mediated by Ants?

PubMed Central

Campos-Navarrete, María José; Abdala-Roberts, Luis; Munguía-Rosas, Miguel A.; Parra-Tabla, Víctor

2015-01-01

Plant diversity can influence predators and omnivores and such effects may in turn influence herbivores and plants. However, evidence for these ecological feedbacks is rare. We evaluated if the effects of tree species (SD) and genotypic diversity (GD) on the abundance of different guilds of insect herbivores associated with big-leaf mahogany (Swietenia macrophylla) were contingent upon the protective effects of ants tending extra-floral nectaries of this species. This study was conducted within a larger experiment consisting of mahogany monocultures and species polycultures of four species and –within each of these two plot types– mahogany was represented by either one or four maternal families. We selected 24 plots spanning these treatment combinations, 10 mahogany plants/plot, and within each plot experimentally reduced ant abundance on half of the selected plants, and surveyed ant and herbivore abundance. There were positive effects of SD on generalist leaf-chewers and sap-feeders, but for the latter group this effect depended on the ant reduction treatment: SD positively influenced sap-feeders under ambient ant abundance but had no effect when ant abundance was reduced; at the same time, ants had negative effects on sap feeders in monoculture but no effect in polyculture. In contrast, SD did not influence specialist stem-borers or leaf-miners and this effect was not contingent upon ant reduction. Finally, GD did not influence any of the herbivore guilds studied, and such effects did not depend on the ant treatment. Overall, we show that tree species diversity influenced interactions between a focal plant species (mahogany) and ants, and that such effects in turn mediated plant diversity effects on some (sap-feeders) but not all the herbivores guilds studied. Our results suggest that the observed patterns are dependent on the combined effects of herbivore identity, diet breadth, and the source of plant diversity. PMID:26241962

Evaluating β Diversity as a Surrogate for Species Representation at Fine Scale.

PubMed

Beier, Paul; Albuquerque, Fábio

2016-01-01

Species turnover or β diversity is a conceptually attractive surrogate for conservation planning. However, there has been only 1 attempt to determine how well sites selected to maximize β diversity represent species, and that test was done at a scale too coarse (2,500 km2 sites) to inform most conservation decisions. We used 8 plant datasets, 3 bird datasets, and 1 mammal dataset to evaluate whether sites selected to span β diversity will efficiently represent species at finer scale (sites sizes < 1 ha to 625 km2). We used ordinations to characterize dissimilarity in species assemblages (β diversity) among plots (inventory data) or among grid cells (atlas data). We then selected sites to maximize β diversity and used the Species Accumulation Index, SAI, to evaluate how efficiently the surrogate (selecting sites for maximum β diversity) represented species in the same taxon. Across all 12 datasets, sites selected for maximum β diversity represented species with a median efficiency of 24% (i.e., the surrogate was 24% more effective than random selection of sites), and an interquartile range of 4% to 41% efficiency. β diversity was a better surrogate for bird datasets than for plant datasets, and for atlas datasets with 10-km to 14-km grid cells than for atlas datasets with 25-km grid cells. We conclude that β diversity is more than a mere descriptor of how species are distributed on the landscape; in particular β diversity might be useful to maximize the complementarity of a set of sites. Because we tested only within-taxon surrogacy, our results do not prove that β diversity is useful for conservation planning. But our results do justify further investigation to identify the circumstances in which β diversity performs well, and to evaluate it as a cross-taxon surrogate.

Conserving the Stage: Climate Change and the Geophysical Underpinnings of Species Diversity

PubMed Central

Anderson, Mark G.; Ferree, Charles E.

2010-01-01

Conservationists have proposed methods for adapting to climate change that assume species distributions are primarily explained by climate variables. The key idea is to use the understanding of species-climate relationships to map corridors and to identify regions of faunal stability or high species turnover. An alternative approach is to adopt an evolutionary timescale and ask ultimately what factors control total diversity, so that over the long run the major drivers of total species richness can be protected. Within a single climatic region, the temperate area encompassing all of the Northeastern U.S. and Maritime Canada, we hypothesized that geologic factors may take precedence over climate in explaining diversity patterns. If geophysical diversity does drive regional diversity, then conserving geophysical settings may offer an approach to conservation that protects diversity under both current and future climates. Here we tested how well geology predicts the species diversity of 14 US states and three Canadian provinces, using a comprehensive new spatial dataset. Results of linear regressions of species diversity on all possible combinations of 23 geophysical and climatic variables indicated that four geophysical factors; the number of geological classes, latitude, elevation range and the amount of calcareous bedrock, predicted species diversity with certainty (adj. R2 = 0.94). To confirm the species-geology relationships we ran an independent test using 18,700 location points for 885 rare species and found that 40% of the species were restricted to a single geology. Moreover, each geology class supported 5–95 endemic species and chi-square tests confirmed that calcareous bedrock and extreme elevations had significantly more rare species than expected by chance (P<0.0001), strongly corroborating the regression model. Our results suggest that protecting geophysical settings will conserve the stage for current and future biodiversity and may be a robust

Cryptic diversity in a fig wasp community-morphologically differentiated species are sympatric but cryptic species are parapatric.

PubMed

Darwell, C T; Cook, J M

2017-02-01

A key debate in ecology centres on the relative importance of niche and neutral processes in determining patterns of community assembly with particular focus on whether ecologically similar species with similar functional traits are able to coexist. Meanwhile, molecular studies are increasingly revealing morphologically indistinguishable cryptic species with presumably similar ecological roles. Determining the geographic distribution of such cryptic species provides opportunities to contrast predictions of niche vs. neutral models. Discovery of sympatric cryptic species increases alpha diversity and supports neutral models, while documentation of allopatric/parapatric cryptic species increases beta diversity and supports niche models. We tested these predictions using morphological and molecular data, coupled with environmental niche modelling analyses, of a fig wasp community along its 2700-km latitudinal range. Molecular methods increased previous species diversity estimates from eight to eleven species, revealing morphologically cryptic species in each of the four wasp genera studied. Congeneric species pairs that were differentiated by a key morphological functional trait (ovipositor length) coexisted sympatrically over large areas. In contrast, morphologically similar species, with similar ovipositor lengths, typically showed parapatric ranges with very little overlap. Despite parapatric ranges, environmental niche models of cryptic congeneric pairs indicate large regions of potential sympatry, suggesting that competitive processes are important in determining the distributions of ecologically similar species. Niche processes appear to structure this insect community, and cryptic diversity may typically contribute mostly to beta rather than alpha diversity. © 2016 John Wiley & Sons Ltd.

Remote sensing of species diversity using Landsat 8 spectral variables

NASA Astrophysics Data System (ADS)

Madonsela, Sabelo; Cho, Moses Azong; Ramoelo, Abel; Mutanga, Onisimo

2017-11-01

The application of remote sensing in biodiversity estimation has largely relied on the Normalized Difference Vegetation Index (NDVI). The NDVI exploits spectral information from red and near infrared bands of Landsat images and it does not consider canopy background conditions hence it is affected by soil brightness which lowers its sensitivity to vegetation. As such NDVI may be insufficient in explaining tree species diversity. Meanwhile, the Landsat program also collects essential spectral information in the shortwave infrared (SWIR) region which is related to plant properties. The study was intended to: (i) explore the utility of spectral information across Landsat-8 spectrum using the Principal Component Analysis (PCA) and estimate alpha diversity (α-diversity) in the savannah woodland in southern Africa, and (ii) define the species diversity index (Shannon (H‧), Simpson (D2) and species richness (S) - defined as number of species in a community) that best relates to spectral variability on the Landsat-8 Operational Land Imager dataset. We designed 90 m × 90 m field plots (n = 71) and identified all trees with a diameter at breast height (DbH) above 10 cm. H‧, D2 and S were used to quantify tree species diversity within each plot and the corresponding spectral information on all Landsat-8 bands were extracted from each field plot. A stepwise linear regression was applied to determine the relationship between species diversity indices (H‧, D2 and S) and Principal Components (PCs), vegetation indices and Gray Level Co-occurrence Matrix (GLCM) texture layers with calibration (n = 46) and test (n = 23) datasets. The results of regression analysis showed that the Simple Ratio Index derivative had a higher relationship with H‧, D2 and S (r2= 0.36; r2= 0.41; r2= 0.24 respectively) compared to NDVI, EVI, SAVI or their derivatives. Moreover the Landsat-8 derived PCs also had a higher relationship with H‧ and D2 (r2 of 0.36 and 0.35 respectively) than the

Rare Species Support Vulnerable Functions in High-Diversity Ecosystems

PubMed Central

Mouillot, David; Bellwood, David R.; Baraloto, Christopher; Chave, Jerome; Galzin, Rene; Harmelin-Vivien, Mireille; Kulbicki, Michel; Lavergne, Sebastien; Lavorel, Sandra; Mouquet, Nicolas; Paine, C. E. Timothy; Renaud, Julien; Thuiller, Wilfried

2013-01-01

Around the world, the human-induced collapses of populations and species have triggered a sixth mass extinction crisis, with rare species often being the first to disappear. Although the role of species diversity in the maintenance of ecosystem processes has been widely investigated, the role of rare species remains controversial. A critical issue is whether common species insure against the loss of functions supported by rare species. This issue is even more critical in species-rich ecosystems where high functional redundancy among species is likely and where it is thus often assumed that ecosystem functioning is buffered against species loss. Here, using extensive datasets of species occurrences and functional traits from three highly diverse ecosystems (846 coral reef fishes, 2,979 alpine plants, and 662 tropical trees), we demonstrate that the most distinct combinations of traits are supported predominantly by rare species both in terms of local abundance and regional occupancy. Moreover, species that have low functional redundancy and are likely to support the most vulnerable functions, with no other species carrying similar combinations of traits, are rarer than expected by chance in all three ecosystems. For instance, 63% and 98% of fish species that are likely to support highly vulnerable functions in coral reef ecosystems are locally and regionally rare, respectively. For alpine plants, 32% and 89% of such species are locally and regionally rare, respectively. Remarkably, 47% of fish species and 55% of tropical tree species that are likely to support highly vulnerable functions have only one individual per sample on average. Our results emphasize the importance of rare species conservation, even in highly diverse ecosystems, which are thought to exhibit high functional redundancy. Rare species offer more than aesthetic, cultural, or taxonomic diversity value; they disproportionately increase the potential breadth of functions provided by ecosystems across

Scorpions from Mexico: From Species Diversity to Venom Complexity.

PubMed

Santibáñez-López, Carlos E; Francke, Oscar F; Ureta, Carolina; Possani, Lourival D

2015-12-24

Scorpions are among the oldest terrestrial arthropods, which are distributed worldwide, except for Antarctica and some Pacific islands. Scorpion envenomation represents a public health problem in several parts of the world. Mexico harbors the highest diversity of scorpions in the world, including some of the world's medically important scorpion species. The systematics and diversity of Mexican scorpion fauna has not been revised in the past decade; and due to recent and exhaustive collection efforts as part of different ongoing major revisionary systematic projects, our understanding of this diversity has changed compared with previous assessments. Given the presence of several medically important scorpion species, the study of their venom in the country is also important. In the present contribution, the diversity of scorpion species in Mexico is revised and updated based on several new systematic contributions; 281 different species are recorded. Commentaries on recent venomic, ecological and behavioral studies of Mexican scorpions are also provided. A list containing the most important peptides identified from 16 different species is included. A graphical representation of the different types of components found in these venoms is also revised. A map with hotspots showing the current knowledge on scorpion distribution and areas explored in Mexico is also provided.

Scorpions from Mexico: From Species Diversity to Venom Complexity

PubMed Central

Santibáñez-López, Carlos E.; Francke, Oscar F.; Ureta, Carolina; Possani, Lourival D.

2015-01-01

Scorpions are among the oldest terrestrial arthropods, which are distributed worldwide, except for Antarctica and some Pacific islands. Scorpion envenomation represents a public health problem in several parts of the world. Mexico harbors the highest diversity of scorpions in the world, including some of the world’s medically important scorpion species. The systematics and diversity of Mexican scorpion fauna has not been revised in the past decade; and due to recent and exhaustive collection efforts as part of different ongoing major revisionary systematic projects, our understanding of this diversity has changed compared with previous assessments. Given the presence of several medically important scorpion species, the study of their venom in the country is also important. In the present contribution, the diversity of scorpion species in Mexico is revised and updated based on several new systematic contributions; 281 different species are recorded. Commentaries on recent venomic, ecological and behavioral studies of Mexican scorpions are also provided. A list containing the most important peptides identified from 16 different species is included. A graphical representation of the different types of components found in these venoms is also revised. A map with hotspots showing the current knowledge on scorpion distribution and areas explored in Mexico is also provided. PMID:26712787

Helicobacter pylori infection and host cell responses.

PubMed

Di Leo, A; Messa, C; Russo, F; Linsalata, M; Amati, L; Caradonna, L; Pece, S; Pellegrino, N M; Caccavo, D; Antonaci, S; Jirillo, E

1999-11-01

It is well known that Helicobacter pylori is able to colonize the gastric mucosa, causing a chronic and persistent infection with complications, such as peptic ulcer and gastric cancer. This review places emphasis on some epidemiological aspects of Helicobacter pylori infection and its mode of transmission. At the same time, invasive and non-invasive methods of diagnosis of Helicobacter pylori infection are illustrated. More space is devoted to the host response following invasion of the stomach. In this respect, the role played by different growth factors and polyamines in the course of Helicobacter pylori disease is discussed also in relation to the result of eradicating treatment. On the other hand, an accurate description of the host immune responses against Helicobacter pylori organism and/or their components (e.g. lipopolysaccharides) is reported. Finally, since Helicobacter pylori has been classified as a class I carcinogen, current researches are focussed on the Helicobacter pylori-induced carcinogenesis.

Evidence for Conserved Function of γ–Glutamyltranspeptidase in Helicobacter Genus

PubMed Central

Revez, Joana; Javed, Sundus; El-Najjar, Nahed; Anderl, Florian; Hyytiäinen, Heidi; Vuorela, Pia; Gerhard, Markus; Hänninen, Marja-Liisa

2012-01-01

The confounding consequences of Helicobacter bilis infection in experimental mice populations are well recognized, but the role of this bacterium in human diseases is less known. Limited data are available on virulence determinants of this species. In Helicobacter pylori, γ-glutamyltranspeptidase (γGT) contributes to the colonization of the gastric mucosa and to the pathogenesis of peptic ulcer. The role of γGT in H. bilis infections remains unknown. The annotated genome sequence of H. bilis revealed two putative ggt genes and our aim was to characterize these H. bilis γGT paralogues. We performed a phylogenetic analysis to understand the evolution of Helicobacter γGTs and to predict functional activities of these two genes. In addition, both copies of H. bilis γGTs were expressed as recombinant proteins and their biochemical characteristics were analysed. Functional complementation of Esherichia coli deficient in γGT activity and deletion of γGT in H. bilis were performed. Finally, the inhibitory effect of T-cell and gastric cell proliferation by H. bilis γGT was assessed. Our results indicated that one gene is responsible for γGT activity, while the other showed no γGT activity due to lack of autoprocessing. Although both H. bilis and H. pylori γGTs exhibited a similar affinity to L-Glutamine and γ-Glutamyl-p-nitroanilide, the H. bilis γGT was significantly less active. Nevertheless, H. bilis γGT inhibited T-cell proliferation at a similar level to that observed for H. pylori. Finally, we showed a similar suppressive influence of both H. bilis and H. pylori γGTs on AGS cell proliferation mediated by an apoptosis-independent mechanism. Our data suggest a conserved function of γGT in the Helicobacter genus. Since γGT is present only in a few enterohepatic Helicobacter species, its expression appears not to be essential for colonization of the lower gastrointestinal tract, but it could provide metabolic advantages in colonization capability of

Quantifying Species Diversity with a DNA Barcoding-Based Method: Tibetan Moth Species (Noctuidae) on the Qinghai-Tibetan Plateau

PubMed Central

Jin, Qian; Han, Huilin; Hu, XiMin; Li, XinHai; Zhu, ChaoDong; Ho, Simon Y. W.; Ward, Robert D.; Zhang, Ai-bing

2013-01-01

With the ongoing loss of biodiversity, there is a great need for fast and effective ways to assess species richness and diversity: DNA barcoding provides a powerful new tool for this. We investigated this approach by focusing on the Tibetan plateau, which is one of the world's top biodiversity hotspots. There have been few studies of its invertebrates, although they constitute the vast majority of the region's diversity. Here we investigated species diversity of the lepidopteran family Noctuidae, across different environmental gradients, using measurements based on traditional morphology as well as on DNA barcoding. The COI barcode showed an average interspecific K2P distance of , which is about four times larger than the mean intraspecific distance (). Using six diversity indices, we did not detect any significant differences in estimated species diversity between measurements based on traditional morphology and on DNA barcoding. Furthermore, we found strong positive correlations between them, indicating that barcode-based measures of species diversity can serve as a good surrogate for morphology-based measures in most situations tested. Eastern communities were found to have significantly higher diversity than Western ones. Among 22 environmental factors tested, we found that three (precipitation of driest month, precipitation of driest quarter, and precipitation of coldest quarter) were significantly correlated with species diversity. Our results indicate that these factors could be the key ecological factors influencing the species diversity of the lepidopteran family Noctuidae on the Tibetan plateau. PMID:23741330

Does population size affect genetic diversity? A test with sympatric lizard species.

PubMed

Hague, M T J; Routman, E J

2016-01-01

Genetic diversity is a fundamental requirement for evolution and adaptation. Nonetheless, the forces that maintain patterns of genetic variation in wild populations are not completely understood. Neutral theory posits that genetic diversity will increase with a larger effective population size and the decreasing effects of drift. However, the lack of compelling evidence for a relationship between genetic diversity and population size in comparative studies has generated some skepticism over the degree that neutral sequence evolution drives overall patterns of diversity. The goal of this study was to measure genetic diversity among sympatric populations of related lizard species that differ in population size and other ecological factors. By sampling related species from a single geographic location, we aimed to reduce nuisance variance in genetic diversity owing to species differences, for example, in mutation rates or historical biogeography. We compared populations of zebra-tailed lizards and western banded geckos, which are abundant and short-lived, to chuckwallas and desert iguanas, which are less common and long-lived. We assessed population genetic diversity at three protein-coding loci for each species. Our results were consistent with the predictions of neutral theory, as the abundant species almost always had higher levels of haplotype diversity than the less common species. Higher population genetic diversity in the abundant species is likely due to a combination of demographic factors, including larger local population sizes (and presumably effective population sizes), faster generation times and high rates of gene flow with other populations.

Exploring species and site contributions to beta diversity in stream insect assemblages.

PubMed

Heino, Jani; Grönroos, Mira

2017-01-01

It was recently suggested that beta diversity can be partitioned into contributions of single sites to overall beta diversity (LCBD) or into contributions of individual species to overall beta diversity (SCBD). We explored the relationships of LCBD and SCBD to site and species characteristics, respectively, in stream insect assemblages. We found that LCBD was mostly explained by variation in species richness, with a negative relationship being detected. SCBD was strongly related to various species characteristics, such as occupancy, abundance, niche position and niche breadth, but was only weakly related to biological traits of species. In particular, occupancy and its quadratic terms showed a very strong unimodal relationship with SCBD, suggesting that intermediate species in terms of site occupancy contribute most to beta diversity. Our findings of unravelling the contributions of sites or species to overall beta diversity are of high importance to community ecology, conservation and bioassessment using stream insect assemblages, and may bear some overall generalities to be found in other organism groups.

Old and new challenges in using species diversity for assessing biodiversity

PubMed Central

Chiarucci, Alessandro; Bacaro, Giovanni; Scheiner, Samuel M.

2011-01-01

Although the maintenance of diversity of living systems is critical for ecosystem functioning, the accelerating pace of global change is threatening its preservation. Standardized methods for biodiversity assessment and monitoring are needed. Species diversity is one of the most widely adopted metrics for assessing patterns and processes of biodiversity, at both ecological and biogeographic scales. However, those perspectives differ because of the types of data that can be feasibly collected, resulting in differences in the questions that can be addressed. Despite a theoretical consensus on diversity metrics, standardized methods for its measurement are lacking, especially at the scales needed to monitor biodiversity for conservation and management purposes. We review the conceptual framework for species diversity, examine common metrics, and explore their use for biodiversity conservation and management. Key differences in diversity measures at ecological and biogeographic scales are the completeness of species lists and the ability to include information on species abundances. We analyse the major pitfalls and problems with quantitative measurement of species diversity, look at the use of weighting measures by phylogenetic distance, discuss potential solutions and propose a research agenda to solve the major existing problems. PMID:21768157

Altitudinal Patterns of Species Diversity and Phylogenetic Diversity across Temperate Mountain Forests of Northern China.

PubMed

Zhang, Wenxin; Huang, Dizhou; Wang, Renqing; Liu, Jian; Du, Ning

2016-01-01

The spatial patterns of biodiversity and their underlying mechanisms have been an active area of research for a long time. In this study, a total of 63 samples (20m × 30m) were systematically established along elevation gradients on Mount Tai and Mount Lao, China. We explored altitudinal patterns of plant diversity in the two mountain systems. In order to understand the mechanisms driving current diversity patterns, we used phylogenetic approaches to detect the spatial patterns of phylogenetic diversity and phylogenetic structure along two elevation gradients. We found that total species richness had a monotonically decreasing pattern and tree richness had a unimodal pattern along the elevation gradients in the two study areas. However, altitudinal patterns in shrub richness and herbs richness were not consistent on the two mountains. At low elevation, anthropogenic disturbances contributed to the increase of plant diversity, especially for shrubs and herbs in understory layers, which are more sensitive to changes in microenvironment. The phylogenetic structure of plant communities exhibited an inverted hump-shaped pattern along the elevation gradient on Mount Tai, which demonstrates that environmental filtering is the main driver of plant community assembly at high and low elevations and inter-specific competition may be the main driver of plant community assembly in the middle elevations. However, the phylogenetic structure of plant communities did not display a clear pattern on Mount Lao where the climate is milder. Phylogenetic beta diversity and species beta diversity consistently increased with increasing altitudinal divergence in the two study areas. However, the altitudinal patterns of species richness did not completely mirror phylogenetic diversity patterns. Conservation areas should be selected taking into consideration the preservation of high species richness, while maximizing phylogenetic diversity to improve the potential for diversification in the

Global latitudinal species diversity gradient in deep-sea benthic foraminifera

NASA Astrophysics Data System (ADS)

Culver, Stephen J.; Buzas, Martin A.

2000-02-01

Global scale patterns of species diversity for modern deep-sea benthic foraminifera, an important component of the bathyal and abyssal meiofauna, are examined using comparable data from five studies in the Atlantic, ranging over 138° of latitude from the Norwegian Sea to the Weddell Sea. We show that a pattern of decreasing diversity with increasing latitude characterises both the North and South Atlantic. This pattern is confirmed for the northern hemisphere by independent data from the west-central North Atlantic and the Arctic basin. Species diversity in the North Atlantic northwards from the equator is variable until a sharp fall in the Norwegian Sea (ca. 65°N). In the South Atlantic species diversity drops from a maximum in latitudes less than 30°S and then decreases slightly from 40 to 70°S. For any given latitude, North Atlantic diversity is generally lower than in the South Atlantic. Both ecological and historical factors related to food supply are invoked to explain the formation and maintenance of the latitudinal gradient of deep-sea benthic foraminiferal species diversity. The gradient formed some 36 million years ago when global climatic cooling led to seasonally fluctuating food supply in higher latitudes.

Species and genetic diversity in the genus Drosophila inhabiting the Indian subcontinent.

PubMed

Singh, Bashisth N

2015-06-01

Biodiversity is the sum total of all living things on the earth with particular reference to the profound variety in structure,function and genetic constitution. It includes both number and frequency of species or genes in a given assemblage and the variety of resulting ecosystems in a region. It is usually considered at three different levels: genetic, species and ecological diversities. Genus Drosophila belongs to the family Drosophilidae (class Insecta, order Diptera), characterized by rich species diversity at global level and also in India, which is a megadiverse country. At global level, more than 1500 species have been described and several thousands estimated. Hawaiian Islands are particularly rich in species diversity with more than 500 species which provides a unique opportunity to study evolution in genus Drosophila. About 150 species of Drosophila have been reported from India. Certain species of Drosophila found in India have been investigated for genetic diversity within the species. In this regard, Drosophila ananassae is noteworthy. It is a cosmopolitan and domestic species with common occurrence in India and is endowed with many genetic peculiarities. Population genetics and evolutionary studies in this species have revealed as to how genetic diversity within a species play an important role in adaptation of populations to varying environments. In addition, the work carried on D. melanogaster, D. nasuta, D. bipectinata and certain other species in India has shown that these species vary in degree and pattern of genetic diversity, and have evolved different mechanisms for adjusting to their environments. The ecological adaptations to various kinds of stress studied in certain species of Drosophila inhabiting the Indian subcontinent are also discussed.

Electron microscopic, genetic and protein expression analyses of Helicobacter acinonychis strains from a Bengal tiger.

PubMed

Tegtmeyer, Nicole; Rivas Traverso, Francisco; Rohde, Manfred; Oyarzabal, Omar A; Lehn, Norbert; Schneider-Brachert, Wulf; Ferrero, Richard L; Fox, James G; Berg, Douglas E; Backert, Steffen

2013-01-01

Colonization by Helicobacter species is commonly noted in many mammals. These infections often remain unrecognized, but can cause severe health complications or more subtle host immune perturbations. The aim of this study was to isolate and characterize putative novel Helicobacter spp. from Bengal tigers in Thailand. Morphological investigation (Gram-staining and electron microscopy) and genetic studies (16SrRNA, 23SrRNA, flagellin, urease and prophage gene analyses, RAPD DNA fingerprinting and restriction fragment polymorphisms) as well as Western blotting were used to characterize the isolated Helicobacters. Electron microscopy revealed spiral-shaped bacteria, which varied in length (2.5-6 µm) and contained up to four monopolar sheathed flagella. The 16SrRNA, 23SrRNA, sequencing and protein expression analyses identified novel H. acinonychis isolates closely related to H. pylori. These Asian isolates are genetically very similar to H. acinonychis strains of other big cats (cheetahs, lions, lion-tiger hybrid and other tigers) from North America and Europe, which is remarkable in the context of the great genetic diversity among worldwide H. pylori strains. We also found by immunoblotting that the Bengal tiger isolates express UreaseA/B, flagellin, BabA adhesin, neutrophil-activating protein NapA, HtrA protease, γ-glutamyl-transpeptidase GGT, Slt lytic transglycosylase and two DNA transfer relaxase orthologs that were known from H. pylori, but not the cag pathogenicity island, nor CagA, VacA, SabA, DupA or OipA proteins. These results give fresh insights into H. acinonychis genetics and the expression of potential pathogenicity-associated factors and their possible pathophysiological relevance in related gastric infections.

Electron Microscopic, Genetic and Protein Expression Analyses of Helicobacter acinonychis Strains from a Bengal Tiger

PubMed Central

Tegtmeyer, Nicole; Rivas Traverso, Francisco; Rohde, Manfred; Oyarzabal, Omar A.; Lehn, Norbert; Schneider-Brachert, Wulf; Ferrero, Richard L.; Fox, James G.; Berg, Douglas E.; Backert, Steffen

2013-01-01

Colonization by Helicobacter species is commonly noted in many mammals. These infections often remain unrecognized, but can cause severe health complications or more subtle host immune perturbations. The aim of this study was to isolate and characterize putative novel Helicobacter spp. from Bengal tigers in Thailand. Morphological investigation (Gram-staining and electron microscopy) and genetic studies (16SrRNA, 23SrRNA, flagellin, urease and prophage gene analyses, RAPD DNA fingerprinting and restriction fragment polymorphisms) as well as Western blotting were used to characterize the isolated Helicobacters. Electron microscopy revealed spiral-shaped bacteria, which varied in length (2.5–6 µm) and contained up to four monopolar sheathed flagella. The 16SrRNA, 23SrRNA, sequencing and protein expression analyses identified novel H. acinonychis isolates closely related to H. pylori. These Asian isolates are genetically very similar to H. acinonychis strains of other big cats (cheetahs, lions, lion-tiger hybrid and other tigers) from North America and Europe, which is remarkable in the context of the great genetic diversity among worldwide H. pylori strains. We also found by immunoblotting that the Bengal tiger isolates express UreaseA/B, flagellin, BabA adhesin, neutrophil-activating protein NapA, HtrA protease, γ-glutamyl-transpeptidase GGT, Slt lytic transglycosylase and two DNA transfer relaxase orthologs that were known from H. pylori, but not the cag pathogenicity island, nor CagA, VacA, SabA, DupA or OipA proteins. These results give fresh insights into H. acinonychis genetics and the expression of potential pathogenicity-associated factors and their possible pathophysiological relevance in related gastric infections. PMID:23940723

The relationship between satellite-derived indices and species diversity across African savanna ecosystems

NASA Astrophysics Data System (ADS)

Mapfumo, Ratidzo B.; Murwira, Amon; Masocha, Mhosisi; Andriani, R.

2016-10-01

The ability to use remotely sensed diversity is important for the management of ecosystems at large spatial extents. However, to achieve this, there is still need to develop robust methods and approaches that enable large-scale mapping of species diversity. In this study, we tested the relationship between species diversity measured in situ with the Normalized Difference Vegetation Index (NDVI) and the Coefficient of Variation in the NDVI (CVNDVI) derived from high and medium spatial resolution satellite data at dry, wet and coastal savanna woodlands. We further tested the effect of logging on NDVI along the transects and between transects as disturbance may be a mechanism driving the patterns observed. Overall, the results of this study suggest that high tree species diversity is associated with low and high NDVI and at intermediate levels is associated with low tree species diversity and NDVI. High tree species diversity is associated with high CVNDVI and vice versa and at intermediate levels is associated with high tree species diversity and CVNDVI.

Genetic Diversity of the Two Commercial Tetraploid Cotton Species in the Gossypium Diversity Reference Set.

PubMed

Hinze, Lori L; Gazave, Elodie; Gore, Michael A; Fang, David D; Scheffler, Brian E; Yu, John Z; Jones, Don C; Frelichowski, James; Percy, Richard G

2016-05-01

A diversity reference set has been constructed for the Gossypium accessions in the US National Cotton Germplasm Collection to facilitate more extensive evaluation and utilization of accessions held in the Collection. A set of 105 mapped simple sequence repeat markers was used to study the allelic diversity of 1933 tetraploid Gossypium accessions representative of the range of diversity of the improved and wild accessions of G. hirsutum and G. barbadense. The reference set contained 410 G. barbadense accessions and 1523 G. hirsutum accessions. Observed numbers of polymorphic and private bands indicated a greater diversity in G. hirsutum as compared to G. barbadense as well as in wild-type accessions as compared to improved accessions in both species. The markers clearly differentiated the 2 species. Patterns of diversity within species were observed but not clearly delineated, with much overlap occurring between races and regions of origin for wild accessions and between historical and geographic breeding pools for cultivated accessions. Although the percentage of accessions showing introgression was higher among wild accessions than cultivars in both species, the average level of introgression within individual accessions, as indicated by species-specific bands, was much higher in wild accessions of G. hirsutum than in wild accessions of G. barbadense. The average level of introgression within individual accessions was higher in improved G. barbadense cultivars than in G. hirsutum cultivars. This molecular characterization reveals the levels and distributions of genetic diversity that will allow for better exploration and utilization of cotton genetic resources. Published by Oxford University Press on behalf of the American Genetic Association 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

A Biotin Biosynthesis Gene Restricted to Helicobacter

PubMed Central

Bi, Hongkai; Zhu, Lei; Jia, Jia; Cronan, John E.

2016-01-01

In most bacteria the last step in synthesis of the pimelate moiety of biotin is cleavage of the ester bond of pimeloyl-acyl carrier protein (ACP) methyl ester. The paradigm cleavage enzyme is Escherichia coli BioH which together with the BioC methyltransferase allows synthesis of the pimelate moiety by a modified fatty acid biosynthetic pathway. Analyses of the extant bacterial genomes showed that bioH is absent from many bioC-containing bacteria and is replaced by other genes. Helicobacter pylori lacks a gene encoding a homologue of the known pimeloyl-ACP methyl ester cleavage enzymes suggesting that it encodes a novel enzyme that cleaves this intermediate. We isolated the H. pylori gene encoding this enzyme, bioV, by complementation of an E. coli bioH deletion strain. Purified BioV cleaved the physiological substrate, pimeloyl-ACP methyl ester to pimeloyl-ACP by use of a catalytic triad, each member of which was essential for activity. The role of BioV in biotin biosynthesis was demonstrated using a reconstituted in vitro desthiobiotin synthesis system. BioV homologues seem the sole pimeloyl-ACP methyl ester esterase present in the Helicobacter species and their occurrence only in H. pylori and close relatives provide a target for development of drugs to specifically treat Helicobacter infections. PMID:26868423

Diversity and Distribution of Freshwater Amphipod Species in Switzerland (Crustacea: Amphipoda)

PubMed Central

Altermatt, Florian; Alther, Roman; Fišer, Cene; Jokela, Jukka; Konec, Marjeta; Küry, Daniel; Mächler, Elvira; Stucki, Pascal; Westram, Anja Marie

2014-01-01

Amphipods are key organisms in many freshwater systems and contribute substantially to the diversity and functioning of macroinvertebrate communities. Furthermore, they are commonly used as bioindicators and for ecotoxicological tests. For many areas, however, diversity and distribution of amphipods is inadequately known, which limits their use in ecological and ecotoxicological studies and handicaps conservation initiatives. We studied the diversity and distribution of amphipods in Switzerland (Central Europe), covering four major drainage basins, an altitudinal gradient of>2,500 m, and various habitats (rivers, streams, lakes and groundwater). We provide the first provisional checklist and detailed information on the distribution and diversity of all amphipod species from Switzerland. In total, we found 29 amphipod species. This includes 16 native and 13 non-native species, one of the latter (Orchestia cavimana) reported here for the first time for Switzerland. The diversity is compared to neighboring countries. We specifically discuss species of the genus Niphargus, which are often receiving less attention. We also found evidence of an even higher level of hidden diversity, and the potential occurrence of further cryptic species. This diversity reflects the biogeographic past of Switzerland, and suggests that amphipods are ideally suited to address questions on endemism and adaptive radiations, post-glaciation re-colonization and invasion dynamics as well as biodiversity-ecosystem functioning relationships in aquatic systems. PMID:25354099

Diversity of Riparian Plants among and within Species Shapes River Communities

PubMed Central

Jackrel, Sara L.; Wootton, J. Timothy

2015-01-01

Organismal diversity among and within species may affect ecosystem function with effects transmitting across ecosystem boundaries. Whether recipient communities adjust their composition, in turn, to maximize their function in response to changes in donor composition at these two scales of diversity is unknown. We use small stream communities that rely on riparian subsidies as a model system. We used leaf pack experiments to ask how variation in plants growing beside streams in the Olympic Peninsula of Washington State, USA affects stream communities via leaf subsidies. Leaves from red alder (Alnus rubra), vine maple (Acer cinereus), bigleaf maple (Acer macrophyllum) and western hemlock (Tsuga heterophylla) were assembled in leaf packs to contrast low versus high diversity, and deployed in streams to compare local versus non-local leaf sources at the among and within species scales. Leaves from individuals within species decomposed at varying rates; most notably thin leaves decomposed rapidly. Among deciduous species, vine maple decomposed most rapidly, harbored the least algal abundance, and supported the greatest diversity of aquatic invertebrates, while bigleaf maple was at the opposite extreme for these three metrics. Recipient communities decomposed leaves from local species rapidly: leaves from early successional plants decomposed rapidly in stream reaches surrounded by early successional forest and leaves from later successional plants decomposed rapidly adjacent to later successional forest. The species diversity of leaves inconsistently affected decomposition, algal abundance and invertebrate metrics. Intraspecific diversity of leaf packs also did not affect decomposition or invertebrate diversity. However, locally sourced alder leaves decomposed more rapidly and harbored greater levels of algae than leaves sourced from conspecifics growing in other areas on the Olympic Peninsula, but did not harbor greater aquatic invertebrate diversity. In contrast to

Diversity of Riparian Plants among and within Species Shapes River Communities.

PubMed

Jackrel, Sara L; Wootton, J Timothy

2015-01-01

Organismal diversity among and within species may affect ecosystem function with effects transmitting across ecosystem boundaries. Whether recipient communities adjust their composition, in turn, to maximize their function in response to changes in donor composition at these two scales of diversity is unknown. We use small stream communities that rely on riparian subsidies as a model system. We used leaf pack experiments to ask how variation in plants growing beside streams in the Olympic Peninsula of Washington State, USA affects stream communities via leaf subsidies. Leaves from red alder (Alnus rubra), vine maple (Acer cinereus), bigleaf maple (Acer macrophyllum) and western hemlock (Tsuga heterophylla) were assembled in leaf packs to contrast low versus high diversity, and deployed in streams to compare local versus non-local leaf sources at the among and within species scales. Leaves from individuals within species decomposed at varying rates; most notably thin leaves decomposed rapidly. Among deciduous species, vine maple decomposed most rapidly, harbored the least algal abundance, and supported the greatest diversity of aquatic invertebrates, while bigleaf maple was at the opposite extreme for these three metrics. Recipient communities decomposed leaves from local species rapidly: leaves from early successional plants decomposed rapidly in stream reaches surrounded by early successional forest and leaves from later successional plants decomposed rapidly adjacent to later successional forest. The species diversity of leaves inconsistently affected decomposition, algal abundance and invertebrate metrics. Intraspecific diversity of leaf packs also did not affect decomposition or invertebrate diversity. However, locally sourced alder leaves decomposed more rapidly and harbored greater levels of algae than leaves sourced from conspecifics growing in other areas on the Olympic Peninsula, but did not harbor greater aquatic invertebrate diversity. In contrast to

Toxicosis in Helicobacter Pylori infection - a hypothesis

PubMed Central

BELASCU, MIHAI

2013-01-01

Background and aim We present a new clinical entity in relation to the Helicobacter pylori infection characterized by complex and varied clinical extra-digestive manifestations. Clinical findings such as asthenia, adynamia, sleep disorders, hair and nails modifications, digestive symptoms and heart rhythm disorders describe the clinical aspect of toxicosis associated with Helicobacter pylori infection. Methods The clinical presentation and therapy of patients with Helicobacter pylori infection were analyzed. Results Combined drug therapy: antibiotics + proton pump inhibitors + colloidal bismuth compound determinate remission of the symptoms in the first 3 to 5 days. The characteristic of the relation between Helicobacter pylori and the mucus-epithelial cell complex, the properties of the bacterial cell components, and the inflammatory and immunological response targeting other organs describe the immuno-pathological outbreak of Helicobacter pylori. Conclusion We support the term of toxicosis associated with Helicobacter pylori infection in selected cases. PMID:26527950

Persistent infection of rhesus monkeys with ‘Helicobacter macacae’ and its isolation from an animal with intestinal adenocarcinoma

PubMed Central

Marini, Robert P.; Muthupalani, Sureshkumar; Shen, Zeli; Buckley, Ellen M.; Alvarado, Cynthia; Taylor, Nancy S.; Dewhirst, Floyd E.; Whary, Mark T.; Patterson, Mary M.; Fox, James G.

2010-01-01

A novel helicobacter, ‘Helicobacter macacae’, was previously isolated from a colony of rhesus and cynomolgus monkeys in which diarrhoea from chronic idiopathic colitis was enzootic. A survey performed in a second colony of rhesus monkeys without a history of chronic diarrhoea determined that 57 % were faecal-culture positive for Helicobacter species. Ten years after the survey, one of the animals from which ‘H. macacae’ had been isolated, a 23-year-old, intact male rhesus monkey (Macaca mulatta), presented with partial inappetence and progressive weight loss. Subsequent evaluation of the monkey revealed anaemia, hypoproteinaemia, hypoalbuminaemia and a palpable abdominal mass. Contrast radiography suggested partial intestinal obstruction. The animal was euthanized and a diagnosis was made of intestinal adenocarcinoma of the ileocaecocolic junction with metastasis to regional lymph nodes and liver. Microaerobic culture of caecal tissue yielded a helicobacter organism identified as ‘H. macacae’ by 16S rRNA gene sequencing – the same species of bacteria isolated 10 years previously. The liver, small intestine and colon were also positive by PCR for Helicobacter species. Intestinal adenocarcinoma is the most common malignancy of aged macaques. Faeces or caecal tissue from five out of five monkeys that remained from the original cohort and that were colonized with ‘H. macacae’ in the initial survey were positive for the organism. The apparent persistence of ‘H. macacae’ in these animals, the isolation of the bacterium from animals with colitis and the recognition of the importance of inflammation in carcinogenesis raise the possibility of an aetiological role in the genesis of intestinal adenocarcinoma in aged rhesus monkeys. PMID:20413623

Historical factors shaped species diversity and composition of Salix in eastern Asia.

PubMed

Wang, Qinggang; Su, Xiangyan; Shrestha, Nawal; Liu, Yunpeng; Wang, Siyang; Xu, Xiaoting; Wang, Zhiheng

2017-02-08

Ambient energy, niche conservatism, historical climate stability and habitat heterogeneity hypothesis have been proposed to explain the broad-scale species diversity patterns and species compositions, while their relative importance have been controversial. Here, we assessed the relative contributions of contemporary climate, historical climate changes and habitat heterogeneity in shaping Salix species diversity and species composition in whole eastern Asia as well as mountains and lowlands using linear regressions and distance-based redundancy analyses, respectively. Salix diversity was negatively related with mean annual temperature. Habitat heterogeneity was more important than contemporary climate in shaping Salix diversity patterns, and their relative contributions were different in mountains and lowlands. In contrast, the species composition was strongly influenced by contemporary climate and historical climate change than habitat heterogeneity, and their relative contributions were nearly the same both in mountains and lowlands. Our findings supported niche conservatism and habitat heterogeneity hypotheses, but did not support ambient energy and historical climate stability hypotheses. The diversity pattern and species composition of Salix could not be well-explained by any single hypothesis tested, suggesting that other factors such as disturbance history and diversification rate may be also important in shaping the diversity pattern and composition of Salix species.

Historical factors shaped species diversity and composition of Salix in eastern Asia

PubMed Central

Wang, Qinggang; Su, Xiangyan; Shrestha, Nawal; Liu, Yunpeng; Wang, Siyang; Xu, Xiaoting; Wang, Zhiheng

2017-01-01

Ambient energy, niche conservatism, historical climate stability and habitat heterogeneity hypothesis have been proposed to explain the broad-scale species diversity patterns and species compositions, while their relative importance have been controversial. Here, we assessed the relative contributions of contemporary climate, historical climate changes and habitat heterogeneity in shaping Salix species diversity and species composition in whole eastern Asia as well as mountains and lowlands using linear regressions and distance-based redundancy analyses, respectively. Salix diversity was negatively related with mean annual temperature. Habitat heterogeneity was more important than contemporary climate in shaping Salix diversity patterns, and their relative contributions were different in mountains and lowlands. In contrast, the species composition was strongly influenced by contemporary climate and historical climate change than habitat heterogeneity, and their relative contributions were nearly the same both in mountains and lowlands. Our findings supported niche conservatism and habitat heterogeneity hypotheses, but did not support ambient energy and historical climate stability hypotheses. The diversity pattern and species composition of Salix could not be well-explained by any single hypothesis tested, suggesting that other factors such as disturbance history and diversification rate may be also important in shaping the diversity pattern and composition of Salix species. PMID:28176816

Diversity of fungi associated with roots of Calanthe orchid species in Korea.

PubMed

Park, Myung Soo; Eimes, John A; Oh, Sang Hoon; Suh, Hwa Jung; Oh, Seung-Yoon; Lee, Seobihn; Park, Ki Hyeong; Kwon, Hyuk Joon; Kim, Soo-Young; Lim, Young Woon

2018-01-01

While symbiotic fungi play a key role in the growth of endangered Calanthe orchid species, the relationship between fungal diversity and Calanthe species remains unclear. Here, we surveyed root associated fungal diversity of six Calanthe orchid species by sequencing the internal transcribed spacer (ITS) region using 454 pyrosequencing. Our results revealed that Paraboeremia and Coprinopsis are dominant fungal genera among Calanthe species. In terms of overall relative abundance, Paraboeremia was the most common fungal genus associated with Calanthe roots, followed by Coprinopsis. Overall fungal diversity showed a significant degree of variation depending on both location and Calanthe species. In terms of number of different fungal genera detected within Calanthe species, C. discolor had the most diverse fungal community, with 10 fungal genera detected. This study will contribute toward a better understanding of those fungi that are required for successful cultivation and conservation of Korean Calanthe species.

Exotic species enhance response diversity to land-use change but modify functional composition.

PubMed

Stavert, Jamie R; Pattemore, David E; Gaskett, Anne C; Beggs, Jacqueline R; Bartomeus, Ignasi

2017-08-16

Two main mechanisms may buffer ecosystem functions despite biodiversity loss. First, multiple species could share similar ecological roles, thus providing functional redundancy. Second, species may respond differently to environmental change (response diversity). However, ecosystem function would be best protected when functionally redundant species also show response diversity. This linkage has not been studied directly, so we investigated whether native and exotic pollinator species with similar traits (functional redundancy) differed in abundance (response diversity) across an agricultural intensification gradient. Exotic pollinator species contributed most positive responses, which partially stabilized overall abundance of the pollinator community. However, although some functionally redundant species exhibited response diversity, this was not consistent across functional groups and aggregate abundances within each functional group were rarely stabilized. This shows functional redundancy and response diversity do not always operate in concert. Hence, despite exotic species becoming increasingly dominant in human-modified systems, they cannot replace the functional composition of native species. © 2017 The Author(s).

Amazon plant diversity revealed by a taxonomically verified species list.

PubMed

Cardoso, Domingos; Särkinen, Tiina; Alexander, Sara; Amorim, André M; Bittrich, Volker; Celis, Marcela; Daly, Douglas C; Fiaschi, Pedro; Funk, Vicki A; Giacomin, Leandro L; Goldenberg, Renato; Heiden, Gustavo; Iganci, João; Kelloff, Carol L; Knapp, Sandra; Cavalcante de Lima, Haroldo; Machado, Anderson F P; Dos Santos, Rubens Manoel; Mello-Silva, Renato; Michelangeli, Fabián A; Mitchell, John; Moonlight, Peter; de Moraes, Pedro Luís Rodrigues; Mori, Scott A; Nunes, Teonildes Sacramento; Pennington, Terry D; Pirani, José Rubens; Prance, Ghillean T; de Queiroz, Luciano Paganucci; Rapini, Alessandro; Riina, Ricarda; Rincon, Carlos Alberto Vargas; Roque, Nádia; Shimizu, Gustavo; Sobral, Marcos; Stehmann, João Renato; Stevens, Warren D; Taylor, Charlotte M; Trovó, Marcelo; van den Berg, Cássio; van der Werff, Henk; Viana, Pedro Lage; Zartman, Charles E; Forzza, Rafaela Campostrini

2017-10-03

Recent debates on the number of plant species in the vast lowland rain forests of the Amazon have been based largely on model estimates, neglecting published checklists based on verified voucher data. Here we collate taxonomically verified checklists to present a list of seed plant species from lowland Amazon rain forests. Our list comprises 14,003 species, of which 6,727 are trees. These figures are similar to estimates derived from nonparametric ecological models, but they contrast strongly with predictions of much higher tree diversity derived from parametric models. Based on the known proportion of tree species in neotropical lowland rain forest communities as measured in complete plot censuses, and on overall estimates of seed plant diversity in Brazil and in the neotropics in general, it is more likely that tree diversity in the Amazon is closer to the lower estimates derived from nonparametric models. Much remains unknown about Amazonian plant diversity, but this taxonomically verified dataset provides a valid starting point for macroecological and evolutionary studies aimed at understanding the origin, evolution, and ecology of the exceptional biodiversity of Amazonian forests.

Themes and Variations: Regulation of RpoN-Dependent Flagellar Genes across Diverse Bacterial Species

PubMed Central

Tsang, Jennifer; Hoover, Timothy R.

2014-01-01

Flagellar biogenesis in bacteria is a complex process in which the transcription of dozens of structural and regulatory genes is coordinated with the assembly of the flagellum. Although the overall process of flagellar biogenesis is conserved among bacteria, the mechanisms used to regulate flagellar gene expression vary greatly among different bacterial species. Many bacteria use the alternative sigma factor σ 54 (also known as RpoN) to transcribe specific sets of flagellar genes. These bacteria include members of the Epsilonproteobacteria (e.g., Helicobacter pylori and Campylobacter jejuni), Gammaproteobacteria (e.g., Vibrio and Pseudomonas species), and Alphaproteobacteria (e.g., Caulobacter crescentus). This review characterizes the flagellar transcriptional hierarchies in these bacteria and examines what is known about how flagellar gene regulation is linked with other processes including growth phase, quorum sensing, and host colonization. PMID:24672734

Estimating tree species diversity in the savannah using NDVI and woody canopy cover

NASA Astrophysics Data System (ADS)

Madonsela, Sabelo; Cho, Moses Azong; Ramoelo, Abel; Mutanga, Onisimo; Naidoo, Laven

2018-04-01

Remote sensing applications in biodiversity research often rely on the establishment of relationships between spectral information from the image and tree species diversity measured in the field. Most studies have used normalized difference vegetation index (NDVI) to estimate tree species diversity on the basis that it is sensitive to primary productivity which defines spatial variation in plant diversity. The NDVI signal is influenced by photosynthetically active vegetation which, in the savannah, includes woody canopy foliage and grasses. The question is whether the relationship between NDVI and tree species diversity in the savanna depends on the woody cover percentage. This study explored the relationship between woody canopy cover (WCC) and tree species diversity in the savannah woodland of southern Africa and also investigated whether there is a significant interaction between seasonal NDVI and WCC in the factorial model when estimating tree species diversity. To fulfil our aim, we followed stratified random sampling approach and surveyed tree species in 68 plots of 90 m × 90 m across the study area. Within each plot, all trees with diameter at breast height of >10 cm were sampled and Shannon index - a common measure of species diversity which considers both species richness and abundance - was used to quantify tree species diversity. We then extracted WCC in each plot from existing fractional woody cover product produced from Synthetic Aperture Radar (SAR) data. Factorial regression model was used to determine the interaction effect between NDVI and WCC when estimating tree species diversity. Results from regression analysis showed that (i) WCC has a highly significant relationship with tree species diversity (r2 = 0.21; p < 0.01), (ii) the interaction between the NDVI and WCC is not significant, however, the factorial model significantly reduced the error of prediction (RMSE = 0.47, p < 0.05) compared to NDVI (RMSE = 0.49) or WCC (RMSE = 0.49) model during

The Impact of Helicobacter pylori Infection on the Gastric Microbiota of the Rhesus Macaque

PubMed Central

Martin, Miriam E.; Bhatnagar, Srijak; George, Michael D.; Paster, Bruce J.; Canfield, Don R.; Eisen, Jonathan A.; Solnick, Jay V.

2013-01-01

Helicobacter pylori colonization is highly prevalent among humans and causes significant gastric disease in a subset of those infected. When present, this bacterium dominates the gastric microbiota of humans and induces antimicrobial responses in the host. Since the microbial context of H. pylori colonization influences the disease outcome in a mouse model, we sought to assess the impact of H. pylori challenge upon the pre-existing gastric microbial community members in the rhesus macaque model. Deep sequencing of the bacterial 16S rRNA gene identified a community profile of 221 phylotypes that was distinct from that of the rhesus macaque distal gut and mouth, although there were taxa in common. High proportions of both H. pylori and H. suis were observed in the post-challenge libraries, but at a given time, only one Helicobacter species was dominant. However, the relative abundance of non-Helicobacter taxa was not significantly different before and after challenge with H. pylori. These results suggest that while different gastric species may show competitive exclusion in the gastric niche, the rhesus gastric microbial community is largely stable despite immune and physiological changes due to H. pylori infection. PMID:24116104

Soil type and species diversity influence selection on physiology in Panicum virgatum

USDA-ARS?s Scientific Manuscript database

Species diversity influences the productivity and stability of plant communities, but its effect on the evolution of species within those communities is poorly understood. In this study, we tested whether species diversity and soil type influence selection on physiology in switchgrass (Panicum virga...

Species Diversity and Bird Feed in Residential Complex

NASA Astrophysics Data System (ADS)

Hadinoto; Suhesti, Eni

2017-12-01

Bird is one component of the ecosystem which has an important role in supporting the occurrence of an organism's life cycle. Therefore, the presence of birds in an area is important, because it can affect the existence and distribution of plant species. The purpose of this study is to calculate the diversity of bird species and identify the source of bird feed in the compound. This study was conducted by field surveys in the residential complex. In addition to the birds as a research object vegetation as habitat / foraging birds were also observed. Data were analyzed by using the bird diversity index, richenes index, bundance index, dominance analysis, analysis of bird distribution and analysis of the level of meeting types, while vegetation will be analyzed based on the type and part of what is eaten by birds. In Pandau Jaya housing complex, found as many as 12 species of birds which consists of seven families. Bird species often present is Cucak Kutilang (Pycnonotus aurigaster) of 20 individuals, Bondol Peking (Lonchura punctulata) 14 individuals and Perkutut Jawa (Geopelia striata) 10 individuals. Bird species diversity (H ‘) in Pandau Jaya housing complex is still relatively moderate with a value of 2.27, while the Evenness Index (E) of 0.91 and Richenes Index (R) of 2.45. Types of vegetation as a food source, among others: mango, guava, cherry, jackfruit, ketapang, coconut, areca, palm, banana, papaya, flowers and grasses.

Pathogenic properties of enterohepatic Helicobacter spp. isolated from rhesus macaques with intestinal adenocarcinoma

PubMed Central

Lertpiriyapong, Kvin; Handt, Laurence; Feng, Yan; Mitchell, Thomas W.; Lodge, Kenneth E.; Shen, Zeli; Dewhirst, Floyd E.; Muthupalani, Sureshkumar

2014-01-01

Considerable progress has been made in understanding the roles of Helicobacter pylori in inflammation and gastric cancer; however, far less is known about the roles of enterohepatic Helicobacter species (EHS) in carcinogenesis and their zoonotic or pathogenic potential. We determined the prevalence of EHS infection in a cohort of geriatric rhesus monkeys in which intestinal adenocarcinoma (IAC) is common and investigated the association between EHS infection and IAC. The cohort consisted of 36 animals, 14 of which (age 26–35 years) had IAC. Of the 36 rhesus, 35 (97 %) were positive for EHS using PCR or bacterial isolation from faeces, colonic or tumour tissues. Only a single rhesus, which had IAC, was negative for EHS by all detection methods. The EHS identified by 16S rRNA sequencing in this study were from three Helicobacter taxa: Helicobacter macacae (previously rhesus monkey taxon 1), Helicobacter sp. rhesus monkey taxon 2, previously described from strain MIT 99-5507, and Helicobacter sp. rhesus monkey taxon 4, related to Helicobacter fennelliae. Thirteen of 14 monkeys with IAC were positive for either H. macacae (7/13, 54 %), EHS rhesus monkey taxon 4 (4/13, 31 %) or a mixture of the two EHS (2/13, 15 %). These results indicate that EHS are prevalent among aged rhesus macaques with IAC. Using Helicobacter genus-specific florescent in situ hybridization, EHS were detected on the surface of colonic epithelia of infected monkeys. All Helicobacter isolates, including H. macacae, effectively adhered to, invaded, and significantly induced proinflammatory genes, including IL-8, IL-6, TNF-α and iNOS, while downregulating genes involved in the function of inflammasomes, particularly IL-1β, CASPASE-1, NRLP3, NLRP6 and NLRC4 in the human colonic T84 cell line (P<0.0001). These results suggest that EHS may represent an aetiological agent mediating diarrhoea, chronic inflammation, and possibly intestinal cancer in non-human primates, and may play a role in

Tree species diversity mitigates disturbance impacts on the forest carbon cycle.

PubMed

Silva Pedro, Mariana; Rammer, Werner; Seidl, Rupert

2015-03-01

Biodiversity fosters the functioning and stability of forest ecosystems and, consequently, the provision of crucial ecosystem services that support human well-being and quality of life. In particular, it has been suggested that tree species diversity buffers ecosystems against the impacts of disturbances, a relationship known as the "insurance hypothesis". Natural disturbances have increased across Europe in recent decades and climate change is expected to amplify the frequency and severity of disturbance events. In this context, mitigating disturbance impacts and increasing the resilience of forest ecosystems is of growing importance. We have tested how tree species diversity modulates the impact of disturbance on net primary production and the total carbon stored in living biomass for a temperate forest landscape in Central Europe. Using the simulation model iLand to study the effect of different disturbance regimes on landscapes with varying levels of tree species richness, we found that increasing diversity generally reduces the disturbance impact on carbon storage and uptake, but that this effect weakens or even reverses with successional development. Our simulations indicate a clear positive relationship between diversity and resilience, with more diverse systems experiencing lower disturbance-induced variability in their trajectories of ecosystem functioning. We found that positive effects of tree species diversity are mainly driven by an increase in functional diversity and a modulation of traits related to recolonization and resource usage. The results of our study suggest that increasing tree species diversity could mitigate the effects of intensifying disturbance regimes on ecosystem functioning and improve the robustness of forest carbon storage and the role of forests in climate change mitigation.

Evaluation of Central North American prairie management based on species diversity, life form, and individual species metrics.

PubMed

Brudvig, Lars A; Mabry, Catherine M; Miller, James R; Walker, Tracy A

2007-06-01

Reintroduction of fire and grazing, alone or in combination, has increasingly been recognized as central to the restoration of North American mixed-grass and tallgrass prairies. Although ecological studies of these systems are abundant, they have generally been observational, or if experimental, have focused on plant species diversity. Species diversity measures alone are not sufficient to inform management, which often has goals associated with life-form groups and individual species. We examined the effects of prescribed fire, light cattle grazing, and a combination of fire and grazing on three vegetation components: species diversity, groups of species categorized by life-form, and individual species. We evaluated how successful these three treatments were in achieving specific management goals for prairies in the Iowa Loess Hills (U.S.A.). The grazing treatment promoted the greatest overall species richness, whereas grazing and burning and grazing treatments resulted in the lowest cover by woody species. Burning alone best achieved the management goals of increasing the cover and diversity of native species and reducing exotic forb and (predominantly exotic) cool-season grass cover. Species-specific responses to treatments appeared idiosyncratic (i.e., within each treatment there existed a set of species attaining their highest frequency) and nearly half of uncommon species were present in only one treatment. Because all management goals were not achieved by any one treatment, we conclude that management in this region may need refining. We suggest that a mosaic of burning and grazing (alone and in combination) may provide the greatest landscape-level species richness; however, this strategy would also likely promote the persistence of exotic species. Our results support the need to consider multiple measures, including species-specific responses, when planning and evaluating management.

Equilibrium Bird Species Diversity in Atlantic Islands.

PubMed

Valente, Luis; Illera, Juan Carlos; Havenstein, Katja; Pallien, Tamara; Etienne, Rampal S; Tiedemann, Ralph

2017-06-05

Half a century ago, MacArthur and Wilson proposed that the number of species on islands tends toward a dynamic equilibrium diversity around which species richness fluctuates [1]. The current prevailing view in island biogeography accepts the fundamentals of MacArthur and Wilson's theory [2] but questions whether their prediction of equilibrium can be fulfilled over evolutionary timescales, given the unpredictable and ever-changing nature of island geological and biotic features [3-7]. Here we conduct a complete molecular phylogenetic survey of the terrestrial bird species from four oceanic archipelagos that make up the diverse Macaronesian bioregion-the Azores, the Canary Islands, Cape Verde, and Madeira [8, 9]. We estimate the times at which birds colonized and speciated in the four archipelagos, including many previously unsampled endemic and non-endemic taxa and their closest continental relatives. We develop and fit a new multi-archipelago dynamic stochastic model to these data, explicitly incorporating information from 91 taxa, both extant and extinct. Remarkably, we find that all four archipelagos have independently achieved and maintained a dynamic equilibrium over millions of years. Biogeographical rates are homogeneous across archipelagos, except for the Canary Islands, which exhibit higher speciation and colonization. Our finding that the avian communities of the four Macaronesian archipelagos display an equilibrium diversity pattern indicates that a diversity plateau may be rapidly achieved on islands where rates of in situ radiation are low and extinction is high. This study reveals that equilibrium processes may be more prevalent than recently proposed, supporting MacArthur and Wilson's 50-year-old theory. Copyright © 2017 Elsevier Ltd. All rights reserved.

Species richness and trophic diversity increase decomposition in a co-evolved food web.

PubMed

Baiser, Benjamin; Ardeshiri, Roxanne S; Ellison, Aaron M

2011-01-01

Ecological communities show great variation in species richness, composition and food web structure across similar and diverse ecosystems. Knowledge of how this biodiversity relates to ecosystem functioning is important for understanding the maintenance of diversity and the potential effects of species losses and gains on ecosystems. While research often focuses on how variation in species richness influences ecosystem processes, assessing species richness in a food web context can provide further insight into the relationship between diversity and ecosystem functioning and elucidate potential mechanisms underpinning this relationship. Here, we assessed how species richness and trophic diversity affect decomposition rates in a complete aquatic food web: the five trophic level web that occurs within water-filled leaves of the northern pitcher plant, Sarracenia purpurea. We identified a trophic cascade in which top-predators--larvae of the pitcher-plant mosquito--indirectly increased bacterial decomposition by preying on bactivorous protozoa. Our data also revealed a facultative relationship in which larvae of the pitcher-plant midge increased bacterial decomposition by shredding detritus. These important interactions occur only in food webs with high trophic diversity, which in turn only occur in food webs with high species richness. We show that species richness and trophic diversity underlie strong linkages between food web structure and dynamics that influence ecosystem functioning. The importance of trophic diversity and species interactions in determining how biodiversity relates to ecosystem functioning suggests that simply focusing on species richness does not give a complete picture as to how ecosystems may change with the loss or gain of species.

Species Richness and Trophic Diversity Increase Decomposition in a Co-Evolved Food Web

PubMed Central

Baiser, Benjamin; Ardeshiri, Roxanne S.; Ellison, Aaron M.

2011-01-01

Ecological communities show great variation in species richness, composition and food web structure across similar and diverse ecosystems. Knowledge of how this biodiversity relates to ecosystem functioning is important for understanding the maintenance of diversity and the potential effects of species losses and gains on ecosystems. While research often focuses on how variation in species richness influences ecosystem processes, assessing species richness in a food web context can provide further insight into the relationship between diversity and ecosystem functioning and elucidate potential mechanisms underpinning this relationship. Here, we assessed how species richness and trophic diversity affect decomposition rates in a complete aquatic food web: the five trophic level web that occurs within water-filled leaves of the northern pitcher plant, Sarracenia purpurea. We identified a trophic cascade in which top-predators — larvae of the pitcher-plant mosquito — indirectly increased bacterial decomposition by preying on bactivorous protozoa. Our data also revealed a facultative relationship in which larvae of the pitcher-plant midge increased bacterial decomposition by shredding detritus. These important interactions occur only in food webs with high trophic diversity, which in turn only occur in food webs with high species richness. We show that species richness and trophic diversity underlie strong linkages between food web structure and dynamics that influence ecosystem functioning. The importance of trophic diversity and species interactions in determining how biodiversity relates to ecosystem functioning suggests that simply focusing on species richness does not give a complete picture as to how ecosystems may change with the loss or gain of species. PMID:21673992

Helicobacter pylori Infection in Rural and Urban Dyspeptic Patients from Venezuela

PubMed Central

Contreras, Monica; Fernández-Delgado, Milagro; Reyes, Nelson; García-Amado, María Alexandra; Rojas, Héctor; Michelangeli, Fabian

2015-01-01

The goal of this work was to assess the Helicobacter pylori prevalence in a rural mestizo population and compare it to an urban population from Venezuela. The study was performed in gastric juice samples of 71 dyspeptic patients from Caracas (urban) and 39 from Tucupita (rural), in the Orinoco Delta region. Helicobacter pylori was detected by amplification of 16S rRNA, glmM, and ureA genes in 55.0% patients from urban and 87.2% from rural populations. cagA was found positive in 51% and 62% urban and rural patients, respectively. Non-H. pylori Helicobacter species were not detected in the urban population, but was found in 7.7% of patients in the rural study site. Frequency values of the 16S rRNA, glmM, and ureA genes were higher in the rural population. The odds ratio for each gene was 15.18 for 16S rRNA, 2.34 for glmM, 2.89 for ureA, and 1.53 cagA, showing significant differences except for cagA when gene frequency was compared in both populations. These results demonstrate a higher frequency of H. pylori and gastric non-H. pylori Helicobacter infection in a rural mestizo population with low hygienic standards as compared with city dwellers, representing a potential risk for the development of gastroduodenal diseases. PMID:26195456

Molecular species delimitation methods and population genetics data reveal extensive lineage diversity and cryptic species in Aglaopheniidae (Hydrozoa).

PubMed

Postaire, Bautisse; Magalon, Hélène; Bourmaud, Chloé A-F; Bruggemann, J Henrich

2016-12-01

A comprehensive inventory of global biodiversity would be greatly improved by automating methods for species delimitation. The Automatic Barcode Gap Discovery method, the Poisson tree processes algorithm and the Generalized mixed Yule-coalescent model have been proposed as means of increasing the rate of biodiversity description using single locus data. We applied these methods to explore the diversity within the Aglaopheniidae, a hydrozoan family with many species widely distributed across tropical and temperate oceans. Our analyses revealed widespread cryptic diversity in this family, almost half of the morpho-species presenting several independent evolutionary lineages, as well as support for cases of synonymy. For two common species of this family, Lytocarpia brevirostris and Macrorhynchia phoenicea, we compared the outputs to clustering analyses based on microsatellite data and to nuclear gene phylogenies. For L. brevirostris, microsatellite data were congruent with results of the species delimitation methods, revealing the existence of two cryptic species with Indo-Pacific distribution. For M. phoenicea, all analyses confirmed the presence of two cryptic species within the South-Western Indian Ocean. Our study suggests that the diversity of Aglaopheniidae might be much higher than assumed, likely related to low dispersal capacities. Sequence-based species delimitation methods seem highly valuable to reveal cryptic diversity in hydrozoans; their application in an integrative framework will be very useful in describing the phyletic diversity of these organisms. Copyright © 2016 Elsevier Inc. All rights reserved.

Purification and characterization of Helicobacter mustelae urease.

PubMed Central

Dunn, B E; Sung, C C; Taylor, N S; Fox, J G

1991-01-01

Helicobacter mustelae is a urease-rich bacterium associated with gastritis in ferrets. The ureases of H. mustelae and Helicobacter pylori, a bacterium implicated in human gastritis, share many characteristics. Helicobacter sp. ureases appear to be unique among bacterial enzymes in exhibiting submillimolar Km values and in being composed of two subunits. Images PMID:1879950

Concordance between genetic and species diversity in coral reef fishes across the Pacific Ocean biodiversity gradient.

PubMed

Messmer, Vanessa; Jones, Geoffrey P; Munday, Philip L; Planes, Serge

2012-12-01

The relationship between genetic diversity and species diversity provides insights into biogeography and historic patterns of evolution and is critical for developing contemporary strategies for biodiversity conservation. Although concordant large-scale clines in genetic and species diversity have been described for terrestrial organisms, whether these parameters co-vary in marine species remains largely unknown. We examined patterns of genetic diversity for 11 coral reef fish species sampled at three locations across the Pacific Ocean species diversity gradient (Australia: ∼1600 species; New Caledonia: ∼1400 species; French Polynesia: ∼800 species). Combined genetic diversity for all 11 species paralleled the decline in species diversity from West to East, with French Polynesia exhibiting lowest total haplotype and nucleotide diversities. Haplotype diversity consistently declined toward French Polynesia in all and nucleotide diversity in the majority of species. The French Polynesian population of most species also exhibited significant genetic differentiation from populations in the West Pacific. A number of factors may have contributed to the general positive correlation between genetic and species diversity, including location and time of species origin, vicariance events, reduced gene flow with increasing isolation, and decreasing habitat area from West to East. However, isolation and habitat area, resulting in reduced population size, are likely to be the most influential. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Amazon plant diversity revealed by a taxonomically verified species list

PubMed Central

Cardoso, Domingos; Särkinen, Tiina; Alexander, Sara; Amorim, André M.; Bittrich, Volker; Celis, Marcela; Daly, Douglas C.; Fiaschi, Pedro; Funk, Vicki A.; Giacomin, Leandro L.; Heiden, Gustavo; Iganci, João; Kelloff, Carol L.; Knapp, Sandra; Cavalcante de Lima, Haroldo; Machado, Anderson F. P.; dos Santos, Rubens Manoel; Mello-Silva, Renato; Michelangeli, Fabián A.; Mitchell, John; Moonlight, Peter; de Moraes, Pedro Luís Rodrigues; Mori, Scott A.; Nunes, Teonildes Sacramento; Pennington, Terry D.; Pirani, José Rubens; Prance, Ghillean T.; de Queiroz, Luciano Paganucci; Rapini, Alessandro; Rincon, Carlos Alberto Vargas; Roque, Nádia; Shimizu, Gustavo; Sobral, Marcos; Stehmann, João Renato; Stevens, Warren D.; Taylor, Charlotte M.; Trovó, Marcelo; van den Berg, Cássio; van der Werff, Henk; Viana, Pedro Lage; Zartman, Charles E.; Forzza, Rafaela Campostrini

2017-01-01

Recent debates on the number of plant species in the vast lowland rain forests of the Amazon have been based largely on model estimates, neglecting published checklists based on verified voucher data. Here we collate taxonomically verified checklists to present a list of seed plant species from lowland Amazon rain forests. Our list comprises 14,003 species, of which 6,727 are trees. These figures are similar to estimates derived from nonparametric ecological models, but they contrast strongly with predictions of much higher tree diversity derived from parametric models. Based on the known proportion of tree species in neotropical lowland rain forest communities as measured in complete plot censuses, and on overall estimates of seed plant diversity in Brazil and in the neotropics in general, it is more likely that tree diversity in the Amazon is closer to the lower estimates derived from nonparametric models. Much remains unknown about Amazonian plant diversity, but this taxonomically verified dataset provides a valid starting point for macroecological and evolutionary studies aimed at understanding the origin, evolution, and ecology of the exceptional biodiversity of Amazonian forests. PMID:28923966

The interplay between Campylobacter and Helicobacter species and other gastrointestinal microbiota of commercial broiler chickens

PubMed Central

2014-01-01

Background Poultry represent an important source of foodborne enteropathogens, in particular thermophilic Campylobacter species. Many of these organisms colonize the intestinal tract of broiler chickens as harmless commensals, and therefore, often remain undetected prior to slaughter. The exact reasons for the lack of clinical disease are unknown, but analysis of the gastrointestinal microbiota of broiler chickens may improve our understanding of the microbial interactions with the host. Methods In this study, the fecal microbiota of 31 market-age (56-day old) broiler chickens, from two different farms, was analyzed using high throughput sequencing. The samples were then screened for two emerging human pathogens, Campylobacter concisus and Helicobacter pullorum, using species-specific PCR. Results The gastrointestinal microbiota of chickens was classified into four potential enterotypes, similar to that of humans, where three enterotypes have been identified. The results indicated that variations between farms may have contributed to differences in the microbiota, though each of the four enterotypes were found in both farms suggesting that these groupings did not occur by chance. In addition to the identification of Campylobacter jejuni subspecies doylei and the emerging species, C. concisus, C. upsaliensis and H. pullorum, several differences in the prevalence of human pathogens within these enterotypes were observed. Further analysis revealed microbial taxa with the potential to increase the likelihood of colonization by a number of these pathogens, including C. jejuni. Conclusion Depletion of these taxa and the addition of taxa that compete with these pathogens, may form the basis of competitive exclusion strategies to eliminate them from the gastrointestinal tract of chickens. PMID:24940386

Phylogenetic diversity of plants alters the effect of species richness on invertebrate herbivory

PubMed Central

2013-01-01

Long-standing ecological theory proposes that diverse communities of plants should experience a decrease in herbivory. Yet previous empirical examinations of this hypothesis have revealed that plant species richness increases herbivory in just as many systems as it decreases it. In this study, I ask whether more insight into the role of plant diversity in promoting or suppressing herbivory can be gained by incorporating information about the evolutionary history of species in a community. In an old field system in southern Ontario, I surveyed communities of plants and measured levels of leaf damage on 27 species in 38 plots. I calculated a measure of phylogenetic diversity (PSE) that encapsulates information about the amount of evolutionary history represented in each of the plots and looked for a relationship between levels of herbivory and both species richness and phylogenetic diversity using a generalized linear mixed model (GLMM) that could account for variation in herbivory levels between species. I found that species richness was positively associated with herbivore damage at the plot-level, in keeping with the results from several other recent studies on this question. On the other hand, phylogenetic diversity was associated with decreased herbivory. Importantly, there was also an interaction between species richness and phylogenetic diversity, such that plots with the highest levels of herbivory were plots which had many species but only if those species tended to be closely related to one another. I propose that these results are the consequence of interactions with herbivores whose diets are phylogenetically specialized (for which I introduce the term cladophage), and how phylogenetic diversity may alter their realized host ranges. These results suggest that incorporating a phylogenetic perspective can add valuable additional insight into the role of plant diversity in explaining or predicting levels of herbivory at a whole-community scale. PMID:23825795

Multidimensional effects of biologically synthesized silver nanoparticles in Helicobacter pylori, Helicobacter felis, and human lung (L132) and lung carcinoma A549 cells.

PubMed

Gurunathan, Sangiliyandi; Jeong, Jae-Kyo; Han, Jae Woong; Zhang, Xi-Feng; Park, Jung Hyun; Kim, Jin-Hoi

2015-01-01

Silver nanoparticles (AgNPs) are prominent group of nanomaterials and are recognized for their diverse applications in various health sectors. This study aimed to synthesize the AgNPs using the leaf extract of Artemisia princeps as a bio-reductant. Furthermore, we evaluated the multidimensional effect of the biologically synthesized AgNPs in Helicobacter pylori, Helicobacter felis, and human lung (L132) and lung carcinoma (A549) cells. UV-visible (UV-vis) spectroscopy confirmed the synthesis of AgNPs. X-ray diffraction (XRD) indicated that the AgNPs are specifically indexed to a crystal structure. The results from Fourier transform infrared spectroscopy (FTIR) indicate that biomolecules are involved in the synthesis and stabilization of AgNPs. Dynamic light scattering (DLS) studies showed the average size distribution of the particle between 10 and 40 nm, and transmission electron microscopy (TEM) confirmed that the AgNPs were significantly well separated and spherical with an average size of 20 nm. AgNPs caused dose-dependent decrease in cell viability and biofilm formation and increase in reactive oxygen species (ROS) generation and DNA fragmentation in H. pylori and H. felis. Furthermore, AgNPs induced mitochondrial-mediated apoptosis in A549 cells; conversely, AgNPs had no significant effects on L132 cells. The results from this study suggest that AgNPs could cause cell-specific apoptosis in mammalian cells. Our findings demonstrate that this environmentally friendly method for the synthesis of AgNPs and that the prepared AgNPs have multidimensional effects such as anti-bacterial and anti-biofilm activity against H. pylori and H. felis and also cytotoxic effects against human cancer cells. This report describes comprehensively the effects of AgNPs on bacteria and mammalian cells. We believe that biologically synthesized AgNPs will open a new avenue towards various biotechnological and biomedical applications in the near future.

Multidimensional effects of biologically synthesized silver nanoparticles in Helicobacter pylori, Helicobacter felis, and human lung (L132) and lung carcinoma A549 cells

NASA Astrophysics Data System (ADS)

Gurunathan, Sangiliyandi; Jeong, Jae-Kyo; Han, Jae Woong; Zhang, Xi-Feng; Park, Jung Hyun; Kim, Jin-Hoi

2015-02-01

Silver nanoparticles (AgNPs) are prominent group of nanomaterials and are recognized for their diverse applications in various health sectors. This study aimed to synthesize the AgNPs using the leaf extract of Artemisia princeps as a bio-reductant. Furthermore, we evaluated the multidimensional effect of the biologically synthesized AgNPs in Helicobacter pylori, Helicobacter felis, and human lung (L132) and lung carcinoma (A549) cells. UV-visible (UV-vis) spectroscopy confirmed the synthesis of AgNPs. X-ray diffraction (XRD) indicated that the AgNPs are specifically indexed to a crystal structure. The results from Fourier transform infrared spectroscopy (FTIR) indicate that biomolecules are involved in the synthesis and stabilization of AgNPs. Dynamic light scattering (DLS) studies showed the average size distribution of the particle between 10 and 40 nm, and transmission electron microscopy (TEM) confirmed that the AgNPs were significantly well separated and spherical with an average size of 20 nm. AgNPs caused dose-dependent decrease in cell viability and biofilm formation and increase in reactive oxygen species (ROS) generation and DNA fragmentation in H. pylori and H. felis. Furthermore, AgNPs induced mitochondrial-mediated apoptosis in A549 cells; conversely, AgNPs had no significant effects on L132 cells. The results from this study suggest that AgNPs could cause cell-specific apoptosis in mammalian cells. Our findings demonstrate that this environmentally friendly method for the synthesis of AgNPs and that the prepared AgNPs have multidimensional effects such as anti-bacterial and anti-biofilm activity against H. pylori and H. felis and also cytotoxic effects against human cancer cells. This report describes comprehensively the effects of AgNPs on bacteria and mammalian cells. We believe that biologically synthesized AgNPs will open a new avenue towards various biotechnological and biomedical applications in the near future.

Recurrence of infection and diversity of Helicobacter pylori strains in an adult population in Mexico treated with empirical standard triple therapy.

PubMed

Sánchez Cuén, Jaime Alberto; Irineo Cabrales, Ana Bertha; León Sicairos, Nidia Maribel; Calderón Zamora, Loranda; Monroy Higuera, Luis; Canizalez Román, Vicente Adrián

2017-11-01

After eradication treatment for Helicobacter pylori, infection could recur due to recrudescence or re-infection. The objective of this study was to determine the recurrence of Helicobacter pylori infection and identify virulent Helicobacter pylori strains one year after eradication with standard triple therapy. A quasi-experimental study was performed that included a patient population with digestive diseases associated with Helicobacter pylori who had received standard triple therapy. Cultures and Polymerase Chain Reaction was performed on gastric biopsies for strain identification in all patients prior to eradication treatment and those with a positive carbon 14 breath test one year after eradication treatment. Statistical analysis was performed using the student T test and Fisher's exact test, statistical significance was set at 0.05. 128 patients were studied, 51 (39.8%) were male and 77 (60.2%) were female with an average age of 54.8 years (DE 13.8). There was an annual recurrence of Helicobacter pylori infection in 12 (9.3%) patients. An annual re-infection and recrudescence occurred in 9 (7 %) and 3 (2.3%) patients respectively. The recrudescence rate for cagA was 1/30 (3.3%) patients and 2/112 (1.8%) patients for vacA. The re-infection rate for cagA was 3/30 (10%) patients and 6/112 (5.3%) patients for vacA. The recurrence of infection in this study was higher than that recorded in developed countries with a low prevalence of H. pylori and lower than that recorded in developing countries with a higher prevalence of H. pylori. The cagA or vacA s2/m2 strains were isolated after re-infection and recrudescence.

In Vitro Antimicrobial Susceptibility Testing of Helicobacter felis, H. bizzozeronii, and H. salomonis

PubMed Central

Van den Bulck, K.; Decostere, A.; Gruntar, I.; Baele, M.; Krt, B.; Ducatelle, R.; Haesebrouck, F.

2005-01-01

The susceptibilities of Helicobacter felis (15 strains), H. bizzozeronii (7 strains), and H. salomonis (3 strains) to 10 antimicrobial agents were investigated by determination of the MIC using the agar dilution method. No consistent differences were noticed between the different Helicobacter species, which were all highly susceptible to ampicillin, clarithromycin, tetracycline, tylosin, enrofloxacin, gentamicin, and neomycin, as demonstrated by low MICs. Higher MICs were obtained for lincomycin (up to 8 μg/ml) and spectinomycin (up to 4 μg/ml). Two H. felis strains showed a MIC of 16 μg/ml for metronidazole, suggesting acquired resistance to this antimicrobial agent. PMID:15980383

Diversity of the Epsilonproteobacteria Dsb (disulfide bond) systems

PubMed Central

Bocian-Ostrzycka, Katarzyna M.; Grzeszczuk, Magdalena J.; Dziewit, Lukasz; Jagusztyn-Krynicka, Elżbieta K.

2015-01-01

The bacterial proteins of the Dsb family—important components of the post-translational protein modification system—catalyze the formation of disulfide bridges, a process that is crucial for protein structure stabilization and activity. Dsb systems play an essential role in the assembly of many virulence factors. Recent rapid advances in global analysis of bacteria have thrown light on the enormous diversity among bacterial Dsb systems. While the Escherichia coli disulfide bond-forming system is quite well understood, the mechanisms of action of Dsb systems in other bacteria, including members of class Epsilonproteobacteria that contain pathogenic and non-pathogenic bacteria colonizing extremely diverse ecological niches, are poorly characterized. Here we present a review of current knowledge on Epsilonproteobacteria Dsb systems. We have focused on the Dsb systems of Campylobacter spp. and Helicobacter spp. because our knowledge about Dsb proteins of Wolinella and Arcobacter spp. is still scarce and comes mainly from bioinformatic studies. Helicobacter pylori is a common human pathogen that colonizes the gastric epithelium of humans with severe consequences. Campylobacter spp. is a leading cause of zoonotic enteric bacterial infections in most developed and developing nations. We focus on various aspects of the diversity of the Dsb systems and their influence on pathogenicity, particularly because Dsb proteins are considered as potential targets for a new class of anti-virulence drugs to treat human infections by Campylobacter or Helicobacter spp. PMID:26106374

High-throughput sequencing reveals unprecedented diversities of Aspergillus species in outdoor air.

PubMed

Lee, S; An, C; Xu, S; Lee, S; Yamamoto, N

2016-09-01

This study used the Illumina MiSeq to analyse compositions and diversities of Aspergillus species in outdoor air. The seasonal air samplings were performed at two locations in Seoul, South Korea. The results showed the relative abundances of all Aspergillus species combined ranging from 0·20 to 18% and from 0·19 to 21% based on the number of the internal transcribed spacer 1 (ITS1) and β-tubulin (BenA) gene sequences respectively. Aspergillus fumigatus was the most dominant species with the mean relative abundances of 1·2 and 5·5% based on the number of the ITS1 and BenA sequences respectively. A total of 29 Aspergillus species were detected and identified down to the species rank, among which nine species were known opportunistic pathogens. Remarkably, eight of the nine pathogenic species were detected by either one of the two markers, suggesting the need of using multiple markers and/or primer pairs when the assessments are made based on the high-throughput sequencing. Due to diversity of species within the genus Aspergillus, the high-throughput sequencing was useful to characterize their compositions and diversities in outdoor air, which are thought to be difficult to be accurately characterized by conventional culture and/or Sanger sequencing-based techniques. Aspergillus is a diverse genus of fungi with more than 300 species reported in literature. Aspergillus is important since some species are known allergens and opportunistic human pathogens. Traditionally, growth-dependent methods have been used to detect Aspergillus species in air. However, these methods are limited in the number of isolates that can be analysed for their identities, resulting in inaccurate characterizations of Aspergillus diversities. This study used the high-throughput sequencing to explore Aspergillus diversities in outdoor, which are thought to be difficult to be accurately characterized by traditional growth-dependent techniques. © 2016 The Society for Applied Microbiology.

Habitat predictors of genetic diversity for two sympatric wetland-breeding amphibian species.

PubMed

McKee, Anna M; Maerz, John C; Smith, Lora L; Glenn, Travis C

2017-08-01

Population genetic diversity is widely accepted as important to the conservation and management of wildlife. However, habitat features may differentially affect evolutionary processes that facilitate population genetic diversity among sympatric species. We measured genetic diversity for two pond-breeding amphibian species (Dwarf salamanders, Eurycea quadridigitata ; and Southern Leopard frogs, Lithobates sphenocephalus ) to understand how habitat characteristics and spatial scale affect genetic diversity across a landscape. Samples were collected from wetlands on a longleaf pine reserve in Georgia. We genotyped microsatellite loci for both species to assess population structures and determine which habitat features were most closely associated with observed heterozygosity and rarefied allelic richness. Both species exhibited significant population genetic structure; however, structure in Southern Leopard frogs was driven primarily by one outlier site. Dwarf salamander allelic richness was greater at sites with less surrounding road area within 0.5 km and more wetland area within 1.0 and 2.5 km, and heterozygosity was greater at sites with more wetland area within 0.5 km. In contrast, neither measure of Southern Leopard frog genetic diversity was associated with any habitat features at any scale we evaluated. Genetic diversity in the Dwarf salamander was strongly associated with land cover variables up to 2.5 km away from breeding wetlands, and/or results suggest that minimizing roads in wetland buffers may be beneficial to the maintenance of population genetic diversity. This study suggests that patterns of genetic differentiation and genetic diversity have associations with different habitat features across different spatial scales for two syntopic pond-breeding amphibian species.

Species diversity and predation strategies in a multiple species predator-prey model

NASA Astrophysics Data System (ADS)

Mullan, Rory; Glass, David H.; McCartney, Mark

2015-08-01

A single predator, single prey ecological model, in which the behaviour of the populations relies upon two control parameters has been expanded to allow for multiple predators and prey to occupy the ecosystem. The diversity of the ecosystem that develops as the model runs is analysed by assessing how many predator or prey species survive. Predation strategies that dictate how the predators distribute their efforts across the prey are introduced in this multiple species model. The paper analyses various predation strategies and highlights their effect on the survival of the predators and prey species.

Woody plant phylogenetic diversity mediates bottom-up control of arthropod biomass in species-rich forests.

PubMed

Schuldt, Andreas; Baruffol, Martin; Bruelheide, Helge; Chen, Simon; Chi, Xiulian; Wall, Marcus; Assmann, Thorsten

2014-09-01

Global change is predicted to cause non-random species loss in plant communities, with consequences for ecosystem functioning. However, beyond the simple effects of plant species richness, little is known about how plant diversity and its loss influence higher trophic levels, which are crucial to the functioning of many species-rich ecosystems. We analyzed to what extent woody plant phylogenetic diversity and species richness contribute to explaining the biomass and abundance of herbivorous and predatory arthropods in a species-rich forest in subtropical China. The biomass and abundance of leaf-chewing herbivores, and the biomass dispersion of herbivores within plots, increased with woody plant phylogenetic diversity. Woody plant species richness had much weaker effects on arthropods, but interacted with plant phylogenetic diversity to negatively affect the ratio of predator to herbivore biomass. Overall, our results point to a strong bottom-up control of functionally important herbivores mediated particularly by plant phylogenetic diversity, but do not support the general expectation that top-down predator effects increase with plant diversity. The observed effects appear to be driven primarily by increasing resource diversity rather than diversity-dependent primary productivity, as the latter did not affect arthropods. The strong effects of plant phylogenetic diversity and the overall weaker effects of plant species richness show that the diversity-dependence of ecosystem processes and interactions across trophic levels can depend fundamentally on non-random species associations. This has important implications for the regulation of ecosystem functions via trophic interaction pathways and for the way species loss may impact these pathways in species-rich forests.

Functional-diversity indices can be driven by methodological choices and species richness.

PubMed

Poos, Mark S; Walker, Steven C; Jackson, Donald A

2009-02-01

Functional diversity is an important concept in community ecology because it captures information on functional traits absent in measures of species diversity. One popular method of measuring functional diversity is the dendrogram-based method, FD. To calculate FD, a variety of methodological choices are required, and it has been debated about whether biological conclusions are sensitive to such choices. We studied the probability that conclusions regarding FD were sensitive, and that patterns in sensitivity were related to alpha and beta components of species richness. We developed a randomization procedure that iteratively calculated FD by assigning species into two assemblages and calculating the probability that the community with higher FD varied across methods. We found evidence of sensitivity in all five communities we examined, ranging from a probability of sensitivity of 0 (no sensitivity) to 0.976 (almost completely sensitive). Variations in these probabilities were driven by differences in alpha diversity between assemblages and not by beta diversity. Importantly, FD was most sensitive when it was most useful (i.e., when differences in alpha diversity were low). We demonstrate that trends in functional-diversity analyses can be largely driven by methodological choices or species richness, rather than functional trait information alone.

Species Diversity of Hypogeous Ascomycetes in Israel

PubMed Central

Wasser, Solomon P.

2010-01-01

We conducted a species diversity study of the hypogeous Ascomycetes of Israel. The hypogeous Ascomycetes in Israel include members of the families Pyronemataceae, Pezizaceae, and Tuberaceae, which are represented by seven species: Hydnocystis piligera, Terfezia arenaria, T. claveryi, T. oligosperma, Tirmania africana, Tuber asa, and T. nitidum; only T. asa is new to Israeli mycobiota. Synonymy, locations, collection data, general distribution, distribution in Israel, descriptions, a key to identification, illustrations, and taxonomic remarks are provided. PMID:23956647

Patterns and controlling factors of species diversity in the Arctic Ocean

USGS Publications Warehouse

Yasuhara, Moriaki; Hunt, Gene; van Dijken, Gert; Arrigo, Kevin R.; Cronin, Thomas M.; Wollenburg, Jutta E.

2012-01-01

Aim  The Arctic Ocean is one of the last near-pristine regions on Earth, and, although human activities are expected to impact on Arctic ecosystems, we know very little about baseline patterns of Arctic Ocean biodiversity. This paper aims to describe Arctic Ocean-wide patterns of benthic biodiversity and to explore factors related to the large-scale species diversity patterns.Location  Arctic Ocean.Methods  We used large ostracode and foraminiferal datasets to describe the biodiversity patterns and applied comprehensive ecological modelling to test the degree to which these patterns are potentially governed by environmental factors, such as temperature, productivity, seasonality, ice cover and others. To test environmental control of the observed diversity patterns, subsets of samples for which all environmental parameters were available were analysed with multiple regression and model averaging.Results  Well-known negative latitudinal species diversity gradients (LSDGs) were found in metazoan Ostracoda, but the LSDGs were unimodal with an intermediate maximum with respect to latitude in protozoan foraminifera. Depth species diversity gradients were unimodal, with peaks in diversity shallower than those in other oceans. Our modelling results showed that several factors are significant predictors of diversity, but the significant predictors were different among shallow marine ostracodes, deep-sea ostracodes and deep-sea foraminifera.Main conclusions  On the basis of these Arctic Ocean-wide comprehensive datasets, we document large-scale diversity patterns with respect to latitude and depth. Our modelling results suggest that the underlying mechanisms causing these species diversity patterns are unexpectedly complex. The environmental parameters of temperature, surface productivity, seasonality of productivity, salinity and ice cover can all play a role in shaping large-scale diversity patterns, but their relative importance may depend on the ecological

Saccharomyces boulardii administration can inhibit the formation of gastric lymphoid follicles induced by Helicobacter suis infection.

PubMed

Yang, Lin; Tian, Zi-Bin; Yu, Ya-Nan; Zhang, Cui-Ping; Li, Xiao-Yu; Mao, Tao; Jing, Xue; Zhao, Wen-Jun; Ding, Xue-Li; Yang, Ruo-Ming; Zhang, Shuai-Qing

2017-01-01

Helicobacter suis has a greater tendency to induce gastric mucosa-associated lymphoid tissue lymphoma compared with other Helicobacter species in humans and animals. Saccharomyces boulardii has been established as an adjunct to H. pylori eradication treatment, but the effect of S. boulardii administration alone on Helicobacter infection remains unclear. Here, we found that S. boulardii administration effectively decreased the bacterial load of H. suis and inhibited the formation of lymphoid follicles in the stomach post-infection. The levels of H. suis-specific immunoglobulin A (IgA) and secretory IgA in the gastric juice and small intestinal secretions and the production of mouse β-defensin-3 in the small intestinal secretions were significantly increased by S. boulardii administration at 12 weeks after H. suis infection. In addition, feeding with S. boulardii inhibited the expression of inflammatory cytokines and lymphoid follicle formation-related factors after H. suis infection. These results suggested that S. boulardii may be useful for the prevention and treatment of Helicobacter infection-related diseases in humans. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Large herbivores maintain termite-caused differences in herbaceous species diversity patterns.

PubMed

Okullo, Paul; Moe, Stein R

2012-09-01

Termites and large herbivores affect African savanna plant communities. Both functional groups are also important for nutrient redistribution across the landscape. We conducted an experiment to study how termites and large herbivores, alone and in combination, affect herbaceous species diversity patterns in an African savanna. Herbaceous vegetation on large vegetated Macrotermes mounds (with and without large herbivores) and on adjacent savanna areas (with and without large herbivores) was monitored over three years in Lake Mburo National Park, Uganda. We found substantial differences in species richness, alpha diversity, evenness, and stability between termite mound herbaceous vegetation and adjacent savanna vegetation. Within months of fencing, levels of species richness, evenness, and stability were no longer significantly different between savanna and mounds. However, fencing reduced the cumulative number of species, particularly for forbs, of which 48% of the species were lost. Fencing increased the beta diversity (dissimilarity among plots) on the resource-poor (in terms of both nutrients and soil moisture) savanna areas, while it did not significantly affect beta diversity on the resource-rich termite mounds. While termites cause substantial heterogeneity in savanna vegetation, large herbivores further amplify these differences by reducing beta diversity on the savanna areas. Large herbivores are, however, responsible for the maintenance of a large number of forbs at the landscape level. These findings suggest that the mechanisms underlying the effects of termites and large herbivores on savanna plant communities scale up to shape community structure and dynamics at a landscape level.

Vegetation in Bangalore's Slums: Composition, Species Distribution, Density, Diversity, and History

NASA Astrophysics Data System (ADS)

Gopal, Divya; Nagendra, Harini; Manthey, Michael

2015-06-01

There is widespread acknowledgement of the need for biodiversity and greening to be part of urban sustainability efforts. Yet we know little about greenery in the context of urban poverty, particularly in slums, which constitute a significant challenge for inclusive development in many rapidly growing cities. We assessed the composition, density, diversity, and species distribution of vegetation in 44 slums of Bangalore, India, comparing these to published studies on vegetation diversity in other land-use categories. Most trees were native to the region, as compared to other land-use categories such as parks and streets which are dominated by introduced species. Of the most frequently encountered tree species, Moringa oleifera and Cocos nucifera are important for food, while Ficus religiosa plays a critical cultural and religious role. Tree density and diversity were much lower in slums compared to richer residential neighborhoods. There are also differences in species preferences, with most plant (herb, shrub and vines) species in slums having economic, food, medicinal, or cultural use, while the species planted in richer residential areas are largely ornamental. Historic development has had an impact on species distribution, with older slums having larger sized tree species, while recent slums were dominated by smaller sized tree species with greater economic and food use. Extensive focus on planting trees and plant species with utility value is required in these congested neighborhoods, to provide livelihood support.

Herbivores rescue diversity in warming tundra by modulating trait-dependent species losses and gains.

PubMed

Kaarlejärvi, Elina; Eskelinen, Anu; Olofsson, Johan

2017-09-04

Climate warming is altering the diversity of plant communities but it remains unknown which species will be lost or gained under warming, especially considering interactions with other factors such as herbivory and nutrient availability. Here, we experimentally test effects of warming, mammalian herbivory and fertilization on tundra species richness and investigate how plant functional traits affect losses and gains. We show that herbivory reverses the impact of warming on diversity: in the presence of herbivores warming increases species richness through higher species gains and lower losses, while in the absence of herbivores warming causes higher species losses and thus decreases species richness. Herbivores promote gains of short-statured species under warming, while herbivore removal and fertilization increase losses of short-statured and resource-conservative species through light limitation. Our results demonstrate that both rarity and traits forecast species losses and gains, and mammalian herbivores are essential for preventing trait-dependent extinctions and mitigate diversity loss under warming and eutrophication.Warming can reduce plant diversity but it is unclear which species will be lost or gained under interacting global changes. Kaarlejärvi et al. manipulate temperature, herbivory and nutrients in a tundra system and find that herbivory maintains diversity under warming by reducing species losses and promoting gains.

Species dispersal rates alter diversity and ecosystem stability in pond metacommunities.

PubMed

Howeth, Jennifer G; Leibold, Mathew A

2010-09-01

Metacommunity theory suggests that relationships between diversity and ecosystem stability can be determined by the rate of species dispersal among local communities. The predicted relationships, however, may depend upon the relative strength of local environmental processes and disturbance. Here we evaluate the role of dispersal frequency and local predation perturbations in affecting patterns of diversity and stability in pond plankton metacommunities. Pond metacommunities were composed of three mesocosm communities: one of the three communities maintained constant "press" predation from a selective predator, bluegill sunfish (Lepomis macrochirus); the second community maintained "press" conditions without predation; and the third community experienced recurrent "pulsed" predation from bluegill sunfish. The triads of pond communities were connected at either no, low (0.7%/d), or high (20%/d) planktonic dispersal. Richness and composition of zooplankton and stability of plankton biomass and ecosystem productivity were measured at local and regional spatial scales. Dispersal significantly affected diversity such that local and regional biotas at the low dispersal rate maintained the greatest number of species. The unimodal local dispersal-diversity relationship was predator-dependent, however, as selective press predation excluded species regardless of dispersal. Further, there was no effect of dispersal on beta diversity because predation generated local conditions that selected for distinct community assemblages. Spatial and temporal ecosystem stability responded to dispersal frequency but not predation. Low dispersal destabilized the spatial stability of producer biomass but stabilized temporal ecosystem productivity. The results indicate that selective predation can prevent species augmentation from mass effects but has no apparent influence on stability. Dispersal rates, in contrast, can have significant effects on both species diversity and ecosystem

Using species abundance distribution models and diversity indices for biogeographical analyses

NASA Astrophysics Data System (ADS)

Fattorini, Simone; Rigal, François; Cardoso, Pedro; Borges, Paulo A. V.

2016-01-01

We examine whether Species Abundance Distribution models (SADs) and diversity indices can describe how species colonization status influences species community assembly on oceanic islands. Our hypothesis is that, because of the lack of source-sink dynamics at the archipelago scale, Single Island Endemics (SIEs), i.e. endemic species restricted to only one island, should be represented by few rare species and consequently have abundance patterns that differ from those of more widespread species. To test our hypothesis, we used arthropod data from the Azorean archipelago (North Atlantic). We divided the species into three colonization categories: SIEs, archipelagic endemics (AZEs, present in at least two islands) and native non-endemics (NATs). For each category, we modelled rank-abundance plots using both the geometric series and the Gambin model, a measure of distributional amplitude. We also calculated Shannon entropy and Buzas and Gibson's evenness. We show that the slopes of the regression lines modelling SADs were significantly higher for SIEs, which indicates a relative predominance of a few highly abundant species and a lack of rare species, which also depresses diversity indices. This may be a consequence of two factors: (i) some forest specialist SIEs may be at advantage over other, less adapted species; (ii) the entire populations of SIEs are by definition concentrated on a single island, without possibility for inter-island source-sink dynamics; hence all populations must have a minimum number of individuals to survive natural, often unpredictable, fluctuations. These findings are supported by higher values of the α parameter of the Gambin mode for SIEs. In contrast, AZEs and NATs had lower regression slopes, lower α but higher diversity indices, resulting from their widespread distribution over several islands. We conclude that these differences in the SAD models and diversity indices demonstrate that the study of these metrics is useful for

Effects of fishing and regional species pool on the functional diversity of fish communities.

PubMed

Martins, Gustavo M; Arenas, Francisco; Neto, Ana I; Jenkins, Stuart R

2012-01-01

The potential population and community level impacts of fishing have received considerable attention, but little is known about how fishing influences communities' functional diversity at regional scales. We examined how estimates of functional diversity differed among 25 regions of variable richness and investigated the functional consequences of removing species targeted by commercial fisheries. Our study shows that fishing leads to substantial losses in functional diversity. The magnitude of such loss was, however, reduced in the more speciose regions. Moreover, the removal of commercially targeted species caused a much larger reduction in functional diversity than expected by random species deletions, which was a consequence of the selective nature of fishing for particular species traits. Results suggest that functional redundancy is spatially variable, that richer biotas provide some degree of insurance against the impact of fishing on communities' functional diversity and that fishing predominantly selects for particular species traits. Understanding how fishing impacts community functional diversity is key to predict its effects for biodiversity as well as ecosystem functioning.

Diverse CLE peptides from cyst nematode species

USDA-ARS?s Scientific Manuscript database

Plant CLAVATA3/ESR (CLE)-like peptides play diverse roles in plant growth and development including maintenance of the stem cell population in the root meristem. Small secreted peptides sharing similarity to plant CLE signaling peptides have been isolated from several cyst nematode species including...

Hurricane disturbance and tropical tree species diversity.

PubMed

Vandermeer, J; Granzow de la Cerda, I; Boucher, D; Perfecto, I; Ruiz, J

2000-10-27

The debate over the maintenance of high diversity of tree species in tropical forests centers on the role of tree-fall gaps as a primary source of disturbance. Using a 10-year data series accumulated since Hurricane Joan struck the Caribbean coast of Nicaragua in 1988, we examined the pattern of species accumulation over time and with increased sampling of individuals. Our analysis shows that the pattern after a hurricane differs from the pattern after a simple tree-fall disturbance, and we conclude that pioneers are limited in large disturbances and thus do not suppress other species the way they do in smaller disturbances.

[Maintaining mechanism of species diversity of land plant communities].

PubMed

Shang, Wenyan; Wu, Gang; Fu, Xiao; Liu, Yang

2005-03-01

The maintaining mechanism of species diversity of land plant communities is a key and advancing edge in biodiversity study. Botanists and ecologists have presented many hypotheses and theories with controversies, and no general theory system was available. In this paper, the problem was reviewed mainly on two scales. The first was big spatial scale, aiming at the physical and natural factors that affect the species diversity, including histories and ages of plant communities, gradient changes such as latitude gradient, water gradient, altitude gradient and soil nutrients gradient, area effect, and isolation; and the second was concentrated on a special plant community, and mainly discussed the relationships of biodiversity with biotic factors (primary productivity, relationship between species, and gap dynamics) and abiotic factors (succession, disturbance and spatial heterogeneity, and human activity).

An exactly solvable coarse-grained model for species diversity

NASA Astrophysics Data System (ADS)

Suweis, Samir; Rinaldo, Andrea; Maritan, Amos

2012-07-01

We present novel analytical results concerning ecosystem species diversity that stem from a proposed coarse-grained neutral model based on birth-death processes. The relevance of the problem lies in the urgency for understanding and synthesizing both theoretical results from ecological neutral theory and empirical evidence on species diversity preservation. The neutral model of biodiversity deals with ecosystems at the same trophic level, where per capita vital rates are assumed to be species independent. Closed-form analytical solutions for the neutral theory are obtained within a coarse-grained model, where the only input is the species persistence time distribution. Our results pertain to: the probability distribution function of the number of species in the ecosystem, both in transient and in stationary states; the n-point connected time correlation function; and the survival probability, defined as the distribution of time spans to local extinction for a species randomly sampled from the community. Analytical predictions are also tested on empirical data from an estuarine fish ecosystem. We find that emerging properties of the ecosystem are very robust and do not depend on specific details of the model, with implications for biodiversity and conservation biology.

Woody Species Diversity in Forest Plantations in a Mountainous Region of Beijing, China: Effects of Sampling Scale and Species Selection

PubMed Central

Zhang, Yuxin; Zhang, Shuang; Ma, Keming; Fu, Bojie; Anand, Madhur

2014-01-01

The role of forest plantations in biodiversity conservation has gained more attention in recent years. However, most work on evaluating the diversity of forest plantations focuses only on one spatial scale; thus, we examined the effects of sampling scale on diversity in forest plantations. We designed a hierarchical sampling strategy to collect data on woody species diversity in planted pine (Pinus tabuliformis Carr.), planted larch (Larix principis-rupprechtii Mayr.), and natural secondary deciduous broadleaf forests in a mountainous region of Beijing, China. Additive diversity partition analysis showed that, compared to natural forests, the planted pine forests had a different woody species diversity partitioning pattern at multi-scales (except the Simpson diversity in the regeneration layer), while the larch plantations did not show multi-scale diversity partitioning patterns that were obviously different from those in the natural secondary broadleaf forest. Compare to the natural secondary broadleaf forests, the effects of planted pine forests on woody species diversity are dependent on the sampling scale and layers selected for analysis. Diversity in the planted larch forest, however, was not significantly different from that in the natural forest for all diversity components at all sampling levels. Our work demonstrated that the species selected for afforestation and the sampling scales selected for data analysis alter the conclusions on the levels of diversity supported by plantations. We suggest that a wide range of scales should be considered in the evaluation of the role of forest plantations on biodiversity conservation. PMID:25545860

Legume species differ in the responses of their functional traits to plant diversity.

PubMed

Roscher, Christiane; Schmid, Bernhard; Buchmann, Nina; Weigelt, Alexandra; Schulze, Ernst-Detlef

2011-02-01

Plants can respond to environmental impacts by variation in functional traits, thereby increasing their performance relative to neighbors. We hypothesized that trait adjustment should also occur in response to influences of the biotic environment, in particular different plant diversity of the community. We used 12 legume species as a model and assessed their variation in morphological, physiological, life-history and performance traits in experimental grasslands of different plant species (1, 2, 4, 8, 16 and 60) and functional group (1-4) numbers. Mean trait values and their variation in response to plant diversity varied among legume species and from trait to trait. The tall-growing Onobrychis viciifolia showed little trait variation in response to increasing plant diversity, whereas the species with shorter statures responded in apparently adaptive ways. The formation of longer shoots with elongated internodes, increased biomass allocation to supporting tissue at the cost of leaf mass, reduced branching, higher specific leaf areas and lower foliar δ(13)C values indicated increasing efforts for light acquisition in more diverse communities. Although leaf nitrogen concentrations and shoot biomass:nitrogen ratios were not affected by increasing plant diversity, foliar δ(15)N values of most legumes decreased and the application of the (15)N natural abundance method suggested that they became more reliant on symbiotic N(2) fixation. Some species formed fewer inflorescences and delayed flowering with increasing community diversity. The observed variation in functional traits generally indicated strategies of legumes to optimize light and nutrient capturing, but they were largely species-dependent and only partly attributable to increasing canopy height and community biomass with increasing plant diversity. Thus, the analysis of individual plant species and their adjustment to growth conditions in communities of increasing plant diversity is essential to get a deeper

Genetic diversity of Bromeliaceae species from the Atlantic Forest.

PubMed

Sheu, Y; Cunha-Machado, A S; Gontijo, A B P L; Favoreto, F C; Soares, T B C; Miranda, F D

2017-04-20

The Bromeliaceae family includes a range of species used for many purposes, including ornamental use and use as food, medicine, feed, and fiber. The state of Espírito Santo, Brazil is a center of diversity for this family in the Atlantic Forest. We evaluated the genetic diversity of five populations of the Bromeliaceae family, including specimens of the genera Aechmea, Billbergia (subfamily Bromelioideae), and Pitcairnia (subfamily Pitcairnioidea), all found in the Atlantic Forest and distributed in the state of Espírito Santo. The number of alleles per locus in populations ranged from two to six and the fixation index (F), estimated for some simple sequence repeats in bromeliad populations, was less than zero in all populations. All markers in the Pitcairnia flammea population were in Hardy-Weinberg equilibrium (P < 0.05). Moreover, significant deviations from Hardy-Weinberg equilibrium were observed at some loci in populations of the five bromeliad species. In most cases, this can be attributed to the presence of inbreeding or the Wahlund effect. The genetic diversity indices of five species showed greater allelic richness in P. flammea (3.55). Therefore, we provide useful information for the characterization of genetic diversity in natural populations of Aechmea ramosa, Aechmea nudicaulis, Billbergia horrid, Billbergia euphemia, and P. flammea in Atlantic Forest remnants in the south of Espírito Santo state.

Influence of Helicobacter pylori culture supernatant on the ecological balance of a dual-species oral biofilm.

PubMed

Zhang, Wenling; Deng, Xiaohong; Zhou, Xuedong; Hao, Yuqing; Li, Yuqing

2018-01-01

Dental caries is a chronic progressive disease occurring in the tooth hard tissue due to multiple factors, in which bacteria are the initial cause. Both Streptococcus mutans and Streptococcus sanguinis are main members of oral biofilm. Helicobacter pylori may also be detected in dental plaque, playing an important role in the development of dental caries. The aim of this study was to investigate the effect of H. pylori culture supernatant on S. mutans and S. sanguinis dual-species biofilm and to evaluate its potential ability on affecting dental health. The effect of H. pylori supernatant on single-species and dual-species biofilm was measured by colony forming units counting and fluorescence in situ hybridization (FISH) assay, respectively. The effect of H. pylori supernatant on S. mutans and S. sanguinis extracellular polysaccharides (EPS) production was measured by both confocal laser scanning microscopy observation and anthrone-sulfuric acid method. The effect of H. pylori supernatant on S. mutans gene expression was measured by quantitative real-time PCR (qRT-PCR) assays. H. pylori supernatant could inhibit both S. mutans and S. sanguinis biofilm formation and EPS production. S. sanguinis inhibition rate was significantly higher than that of S. mutans. Finally, S. mutans bacteriocin and acidogenicity related genes expression were affected by H. pylori culture supernatant. Our results showed that H. pylori could destroy the balance between S. mutans and S. sanguinis in oral biofilm, creating an advantageous environment for S. mutans, which became the dominant bacteria, promoting the formation and development of dental caries.

Influence of Helicobacter pylori culture supernatant on the ecological balance of a dual-species oral biofilm

PubMed Central

Zhang, Wenling; Deng, Xiaohong; Zhou, Xuedong; Hao, Yuqing; Li, Yuqing

2018-01-01

Abstract Dental caries is a chronic progressive disease occurring in the tooth hard tissue due to multiple factors, in which bacteria are the initial cause. Both Streptococcus mutans and Streptococcus sanguinis are main members of oral biofilm. Helicobacter pylori may also be detected in dental plaque, playing an important role in the development of dental caries. Objective The aim of this study was to investigate the effect of H. pylori culture supernatant on S. mutans and S. sanguinis dual-species biofilm and to evaluate its potential ability on affecting dental health. Material and methods The effect of H. pylori supernatant on single-species and dual-species biofilm was measured by colony forming units counting and fluorescence in situ hybridization (FISH) assay, respectively. The effect of H. pylori supernatant on S. mutans and S. sanguinis extracellular polysaccharides (EPS) production was measured by both confocal laser scanning microscopy observation and anthrone-sulfuric acid method. The effect of H. pylori supernatant on S. mutans gene expression was measured by quantitative real-time PCR (qRT-PCR) assays. Results H. pylori supernatant could inhibit both S. mutans and S. sanguinis biofilm formation and EPS production. S. sanguinis inhibition rate was significantly higher than that of S. mutans. Finally, S. mutans bacteriocin and acidogenicity related genes expression were affected by H. pylori culture supernatant. Conclusion Our results showed that H. pylori could destroy the balance between S. mutans and S. sanguinis in oral biofilm, creating an advantageous environment for S. mutans, which became the dominant bacteria, promoting the formation and development of dental caries. PMID:29489935

Genetic diversity of Cosmos species revealed by RAPD and ISSR markers.

PubMed

Rodríguez-Bernal, A; Piña-Escutia, J L; Vázquez-García, L M; Arzate-Fernández, A M

2013-12-04

The genus Cosmos is native of America and is constituted by 34 species; 28 of them are endemic of Mexico. The cosmos are used as a nematicide, antimalarial, and antioxidative agent. The aim of this study was to estimate the genetic diversity among 7 cosmos species based on random amplified polymorphic DNA (RAPD) and inter-simple sequences repeats (ISSR) markers. With RAPD markers, the obtained polymorphism was 91.7 % and the genetic diversity was 0.33, whereas these values were 65.6%, and 0.22 from ISSR markers, respectively, indicating the presence of high genetic diversity among the Cosmos species that were analyzed. The unweighted pair group method with arithmetic mean dendrograms that were obtained with both markers were notably similar, revealing 2 clusters and indicating a clear genetic differentiation among the Cosmos species that were assessed. The first cluster comprised the species Cosmos sulphureus, Cosmos pacificus, and Cosmos diversifolius, while the second cluster included the species Cosmos purpureus, Cosmos crithmifolius, Cosmos bipinnatus, and Cosmos parviflorus. Besides this, the Cosmos species were clustered according to their collection sites. The Mantel test corroborates the correlation between the genetic distance and the geographic altitude of each Cosmos species. The results suggest that it is necessary to preserve the Cosmos species in their natural habitat in addition to the germoplasm collection for ex situ conservation.

Complementary effects of species and genetic diversity on productivity and stability of sown grasslands.

PubMed

Prieto, Iván; Violle, Cyrille; Barre, Philippe; Durand, Jean-Louis; Ghesquiere, Marc; Litrico, Isabelle

2015-03-30

Plant species diversity regulates the productivity(1-3) and stability(2,4) of natural ecosystems, along with their resilience to disturbance(5,6). The influence of species diversity on the productivity of agronomic systems is less clear(7-10). Plant genetic diversity is also suspected to influence ecosystem function(3,11-14), although empirical evidence is scarce. Given the large range of genotypes that can be generated per species through artificial selection, genetic diversity is a potentially important leverage of productivity in cultivated systems. Here we assess the effect of species and genetic diversity on the production and sustainable supply of livestock fodder in sown grasslands, comprising single and multispecies assemblages characterized by different levels of genetic diversity, exposed to drought and non-drought conditions. Multispecies assemblages proved more productive than monocultures when subject to drought, regardless of the number of genotypes per species present. Conversely, the temporal stability of production increased only with the number of genotypes present under both drought and non-drought conditions, and was unaffected by the number of species. We conclude that taxonomic and genetic diversity can play complementary roles when it comes to optimizing livestock fodder production in managed grasslands, and suggest that both levels of diversity should be considered in plant breeding programmes designed to boost the productivity and resilience of managed grasslands in the face of increasing environmental hazards.

Species mtDNA genetic diversity explained by infrapopulation size in a host-symbiont system.

PubMed

Doña, Jorge; Moreno-García, Marina; Criscione, Charles D; Serrano, David; Jovani, Roger

2015-12-01

Understanding what shapes variation in genetic diversity among species remains a major challenge in evolutionary ecology, and it has been seldom studied in parasites and other host-symbiont systems. Here, we studied mtDNA variation in a host-symbiont non-model system: 418 individual feather mites from 17 feather mite species living on 17 different passerine bird species. We explored how a surrogate of census size, the median infrapopulation size (i.e., the median number of individual parasites per infected host individual), explains mtDNA genetic diversity. Feather mite species genetic diversity was positively correlated with mean infrapopulation size, explaining 34% of the variation. As expected from the biology of feather mites, we found bottleneck signatures for most of the species studied but, in particular, three species presented extremely low mtDNA diversity values given their infrapopulation size. Their star-like haplotype networks (in contrast with more reticulated networks for the other species) suggested that their low genetic diversity was the consequence of severe bottlenecks or selective sweeps. Our study shows for the first time that mtDNA diversity can be explained by infrapopulation sizes, and suggests that departures from this relationship could be informative of underlying ecological and evolutionary processes.

Saturating effects of species diversity on life-history evolution in bacteria.

PubMed

Fiegna, Francesca; Scheuerl, Thomas; Moreno-Letelier, Alejandra; Bell, Thomas; Barraclough, Timothy G

2015-09-22

Species interactions can play a major role in shaping evolution in new environments. In theory, species interactions can either stimulate evolution by promoting coevolution or inhibit evolution by constraining ecological opportunity. The relative strength of these effects should vary as species richness increases, and yet there has been little evidence for evolution of component species in communities. We evolved bacterial microcosms containing between 1 and 12 species in three different environments. Growth rates and yields of isolates that evolved in communities were lower than those that evolved in monocultures, consistent with recent theory that competition constrains species to specialize on narrower sets of resources. This effect saturated or reversed at higher levels of richness, consistent with theory that directional effects of species interactions should weaken in more diverse communities. Species varied considerably, however, in their responses to both environment and richness levels. Mechanistic models and experiments are now needed to understand and predict joint evolutionary dynamics of species in diverse communities. © 2015 The Authors.

Links between tree species, symbiotic fungal diversity and ecosystem functioning in simplified tropical ecosystems.

PubMed

Lovelock, Catherine E; Ewel, John J

2005-07-01

We studied the relationships among plant and arbuscular mycorrhizal (AM) fungal diversity, and their effects on ecosystem function, in a series of replicate tropical forestry plots in the La Selva Biological Station, Costa Rica. Forestry plots were 12 yr old and were either monocultures of three tree species, or polycultures of the tree species with two additional understory species. Relationships among the AM fungal spore community, host species, plant community diversity and ecosystem phosphorus-use efficiency (PUE) and net primary productivity (NPP) were assessed. Analysis of the relative abundance of AM fungal spores found that host tree species had a significant effect on the AM fungal community, as did host plant community diversity (monocultures vs polycultures). The Shannon diversity index of the AM fungal spore community differed significantly among the three host tree species, but was not significantly different between monoculture and polyculture plots. Over all the plots, significant positive relationships were found between AM fungal diversity and ecosystem NPP, and between AM fungal community evenness and PUE. Relative abundance of two of the dominant AM fungal species also showed significant correlations with NPP and PUE. We conclude that the AM fungal community composition in tropical forests is sensitive to host species, and provide evidence supporting the hypothesis that the diversity of AM fungi in tropical forests and ecosystem NPP covaries.

Consumer preference for seeds and seedlings of rare species impacts tree diversity at multiple scales.

PubMed

Young, Hillary S; McCauley, Douglas J; Guevara, Roger; Dirzo, Rodolfo

2013-07-01

Positive density-dependent seed and seedling predation, where herbivores selectively eat seeds or seedlings of common species, is thought to play a major role in creating and maintaining plant community diversity. However, many herbivores and seed predators are known to exhibit preferences for rare foods, which could lead to negative density-dependent predation. In this study, we first demonstrate the occurrence of increased predation of locally rare tree species by a widespread group of insular seed and seedling predators, land crabs. We then build computer simulations based on these empirical data to examine the effects of such predation on diversity patterns. Simulations show that herbivore preferences for locally rare species are likely to drive scale-dependent effects on plant community diversity: at small scales these foraging patterns decrease plant community diversity via the selective consumption of rare plant species, while at the landscape level they should increase diversity, at least for short periods, by promoting clustered local dominance of a variety of species. Finally, we compared observed patterns of plant diversity at the site to those obtained via computer simulations, and found that diversity patterns generated under simulations were highly consistent with observed diversity patterns. We posit that preference for rare species by herbivores may be prevalent in low- or moderate-diversity systems, and that these effects may help explain diversity patterns across different spatial scales in such ecosystems.

Effects of Fishing and Regional Species Pool on the Functional Diversity of Fish Communities

PubMed Central

Martins, Gustavo M.; Arenas, Francisco; Neto, Ana I.; Jenkins, Stuart R.

2012-01-01

The potential population and community level impacts of fishing have received considerable attention, but little is known about how fishing influences communities’ functional diversity at regional scales. We examined how estimates of functional diversity differed among 25 regions of variable richness and investigated the functional consequences of removing species targeted by commercial fisheries. Our study shows that fishing leads to substantial losses in functional diversity. The magnitude of such loss was, however, reduced in the more speciose regions. Moreover, the removal of commercially targeted species caused a much larger reduction in functional diversity than expected by random species deletions, which was a consequence of the selective nature of fishing for particular species traits. Results suggest that functional redundancy is spatially variable, that richer biotas provide some degree of insurance against the impact of fishing on communities’ functional diversity and that fishing predominantly selects for particular species traits. Understanding how fishing impacts community functional diversity is key to predict its effects for biodiversity as well as ecosystem functioning. PMID:22952950

Comparison of Diagnostic Techniques for Helicobacter cetorum Infection in Wild Atlantic Bottlenose Dolphins (Tursiops truncatus)

PubMed Central

Harper, Claudia G.; Whary, Mark T.; Feng, Yan; Rhinehart, Howard L.; Wells, Randall S.; Xu, Shilu; Taylor, Nancy S.; Fox, James G.

2003-01-01

Helicobacter cetorum sp. nov. has been cultured from the stomach of Atlantic white-sided dolphins (Lagenorhynchus acutus) and the feces of Pacific white-sided (L. obliquidens) and Atlantic bottlenose (Tursiops truncatus) dolphins and a beluga whale (Delphinapterus leucas). H. cetorum has high homology to Helicobacter pylori as shown by 16S rRNA sequencing, and H. cetorum infection has been associated with gastritis and clinical signs in cetaceans. Because the prevalence of H. cetorum in wild populations is unknown, minimally invasive techniques for detecting H. cetorum were compared for 20 wild bottlenose dolphins sampled as part of a long-term health study. Fecal samples were tested for helicobacter by culture, Southern blotting, and PCR using genus-specific and H. cetorum-specific primers. An enzyme-linked immunosorbent assay (ELISA) was developed to measure H. cetorum immunoglobulin G (IgG). H. cetorum was cultured from 4 of 20 fecal samples, 7 samples were positive using Helicobacter sp. PCR, and 8 samples were positive for H. cetorum using species-specific primers. Two additional fecal samples were positive by Helicobacter sp. Southern blotting, suggesting infection with another helicobacter. All 20 sera contained high levels of IgG antibodies to H. cetorum that were significantly lowered by preabsorption of the sera with whole-cell suspensions of H. cetorum (P < 0.02). Until the specificity of the serum ELISA can be determined by testing sera from dolphins confirmed to be uninfected, PCR and Southern blot screenings of feces are the most sensitive techniques for detection of H. cetorum, and results indicate there is at least a 50% prevalence of H. cetorum infection in these dolphins. PMID:12843010

Plant Functional Diversity Can Be Independent of Species Diversity: Observations Based on the Impact of 4-Yrs of Nitrogen and Phosphorus Additions in an Alpine Meadow

PubMed Central

Li, Wei; Cheng, Ji-Min; Yu, Kai-Liang; Epstein, Howard E.; Guo, Liang; Jing, Guang-Hua; Zhao, Jie; Du, Guo-Zhen

2015-01-01

Past studies have widely documented the decrease in species diversity in response to addition of nutrients, however functional diversity is often independent from species diversity. In this study, we conducted a field experiment to examine the effect of nitrogen and phosphorus fertilization ((NH4)2 HPO4) at 0, 15, 30 and 60 g m-2 yr-1 (F0, F15, F30 and F60) after 4 years of continuous fertilization on functional diversity and species diversity, and its relationship with productivity in an alpine meadow community on the Tibetan Plateau. To this purpose, three community-weighted mean trait values (specific leaf area, SLA; mature plant height, MPH; and seed size, SS) for 30 common species in each fertilization level were determined; three components of functional diversity (functional richness, FRic; functional evenness, FEve; and Rao’s index of quadratic entropy, FRao) were quantified. Our results showed that: (i) species diversity sharply decreased, but functional diversity remained stable with fertilization; (ii) community-weighted mean traits (SLA and MPH) had a significant increase along the fertilization level; (iii) aboveground biomass was not correlated with functional diversity, but it was significantly correlated with species diversity and MPH. Our results suggest that decreases in species diversity due to fertilization do not result in corresponding changes in functional diversity. Functional identity of species may be more important than functional diversity in influencing aboveground productivity in this alpine meadow community, and our results also support the mass ratio hypothesis; that is, the traits of the dominant species influenced the community biomass production. PMID:26295345

Plant Functional Diversity Can Be Independent of Species Diversity: Observations Based on the Impact of 4-Yrs of Nitrogen and Phosphorus Additions in an Alpine Meadow.

PubMed

Li, Wei; Cheng, Ji-Min; Yu, Kai-Liang; Epstein, Howard E; Guo, Liang; Jing, Guang-Hua; Zhao, Jie; Du, Guo-Zhen

2015-01-01

Past studies have widely documented the decrease in species diversity in response to addition of nutrients, however functional diversity is often independent from species diversity. In this study, we conducted a field experiment to examine the effect of nitrogen and phosphorus fertilization ((NH4)2 HPO4) at 0, 15, 30 and 60 g m-2 yr-1 (F0, F15, F30 and F60) after 4 years of continuous fertilization on functional diversity and species diversity, and its relationship with productivity in an alpine meadow community on the Tibetan Plateau. To this purpose, three community-weighted mean trait values (specific leaf area, SLA; mature plant height, MPH; and seed size, SS) for 30 common species in each fertilization level were determined; three components of functional diversity (functional richness, FRic; functional evenness, FEve; and Rao's index of quadratic entropy, FRao) were quantified. Our results showed that: (i) species diversity sharply decreased, but functional diversity remained stable with fertilization; (ii) community-weighted mean traits (SLA and MPH) had a significant increase along the fertilization level; (iii) aboveground biomass was not correlated with functional diversity, but it was significantly correlated with species diversity and MPH. Our results suggest that decreases in species diversity due to fertilization do not result in corresponding changes in functional diversity. Functional identity of species may be more important than functional diversity in influencing aboveground productivity in this alpine meadow community, and our results also support the mass ratio hypothesis; that is, the traits of the dominant species influenced the community biomass production.

Can tree species diversity be assessed with Landsat data in a temperate forest?

PubMed

Arekhi, Maliheh; Yılmaz, Osman Yalçın; Yılmaz, Hatice; Akyüz, Yaşar Feyza

2017-10-28

The diversity of forest trees as an indicator of ecosystem health can be assessed using the spectral characteristics of plant communities through remote sensing data. The objectives of this study were to investigate alpha and beta tree diversity using Landsat data for six dates in the Gönen dam watershed of Turkey. We used richness and the Shannon and Simpson diversity indices to calculate tree alpha diversity. We also represented the relationship between beta diversity and remotely sensed data using species composition similarity and spectral distance similarity of sampling plots via quantile regression. A total of 99 sampling units, each 20 m × 20 m, were selected using geographically stratified random sampling method. Within each plot, the tree species were identified, and all of the trees with a diameter at breast height (dbh) larger than 7 cm were measured. Presence/absence and abundance data (tree species number and tree species basal area) of tree species were used to determine the relationship between richness and the Shannon and Simpson diversity indices, which were computed with ground field data, and spectral variables derived (2 × 2 pixels and 3 × 3 pixels) from Landsat 8 OLI data. The Shannon-Weiner index had the highest correlation. For all six dates, NDVI (normalized difference vegetation index) was the spectral variable most strongly correlated with the Shannon index and the tree diversity variables. The Ratio of green to red (VI) was the spectral variable least correlated with the tree diversity variables and the Shannon basal area. In both beta diversity curves, the slope of the OLS regression was low, while in the upper quantile, it was approximately twice the lower quantiles. The Jaccard index is closed to one with little difference in both two beta diversity approaches. This result is due to increasing the similarity between the sampling plots when they are located close to each other. The intercept differences between two

Genetic diversity and structure of the threatened species Sinopodophyllum hexandrum (Royle) Ying.

PubMed

Liu, W; Wang, J; Yin, D X; Yang, M; Wang, P; Han, Q S; Ma, Q Q; Liu, J J; Wang, J X

2016-06-10

Sinopodophyllum hexandrum is an important medicinal plant that has been listed as an endangered species, making the conservation of its genetic diversity a priority. Therefore, the genetic diversity and population structure of S. hexandrum was investigated through inter-simple sequence repeat analysis of eight natural populations. Eleven selected primers generated 141 discernible fragments. The percentage of polymorphic bands was 37.59% at the species level, and 7.66-24.32% at the population level. Genetic diversity of S. hexandrum was low within populations (average HE = 0.0366), but higher at the species level (HE = 0.0963). Clear structure and high genetic differentiation were detected between populations using unweighted pair groups mean arithmetic and principle coordinate analysis. Clustering approaches clustered the eight sampled populations into three major groups, and AMOVA confirmed there to be significant variation between populations (63.27%). Genetic differentiation may have arisen through limited gene flow (Nm = 0.3317) in this species. Isolation by distance among populations was determined by comparing genetic distance versus geographical distance using the Mantel test. The results revealed no correlation between spatial pattern and geographic location. Given the low within-population genetic diversity, high differentiation among populations, and the increasing anthropogenic pressure on this species, in situ conservation measures, in addition to sampling and ex situ preservation, are recommended to preserve S. hexandrum populations and to retain their genetic diversity.

Latitudinal species diversity gradient of marine zooplankton for the last three million years

USGS Publications Warehouse

Yasuhara, Moriaki; Hunt, Gene; Dowsett, Harry J.; Robinson, Marci M.; Stoll, Danielle K.

2012-01-01

High tropical and low polar biodiversity is one of the most fundamental patterns characterising marine ecosystems, and the influence of temperature on such marine latitudinal diversity gradients is increasingly well documented. However, the temporal stability of quantitative relationships among diversity, latitude and temperature is largely unknown. Herein we document marine zooplankton species diversity patterns at four time slices [modern, Last Glacial Maximum (18 000 years ago), last interglacial (120 000 years ago), and Pliocene (~3.3–3.0 million years ago)] and show that, although the diversity-latitude relationship has been dynamic, diversity-temperature relationships are remarkably constant over the past three million years. These results suggest that species diversity is rapidly reorganised as species' ranges respond to temperature change on ecological time scales, and that the ecological impact of future human-induced temperature change may be partly predictable from fossil and paleoclimatological records.

Patterns of Tree Species Diversity in Relation to Climatic Factors on the Sierra Madre Occidental, Mexico

PubMed Central

Silva-Flores, Ramón; Pérez-Verdín, Gustavo; Wehenkel, Christian

2014-01-01

Biological diversity can be defined as variability among living organisms from all sources, including terrestrial organisms, marine and other aquatic ecosystems, and the ecological complexes which they are part of. This includes diversity within species, between species, and of ecosystems. Numerous diversity indices combine richness and evenness in a single expression, and several climate-based explanations have been proposed to explain broad-scale diversity patterns. However, climate-based water-energy dynamics appears to be an essential factor that determines patterns of diversity. The Mexican Sierra Madre Occidental occupies an area of about 29 million hectares and is located between the Neotropical and Holarctic ecozones. It shelters a high diversity of flora, including 24 different species of Pinus (ca. 22% on the whole), 54 species of Quercus (ca. 9–14%), 7 species of Arbutus (ca. 50%) and many other trees species. The objectives of this study were to model how tree species diversity is related to climatic and geographic factors and stand density and to test the Metabolic Theory, Productivity-Diversity Hypothesis, Physiological Tolerance Hypothesis, Mid-Domain Effect, and the Water-Energy Dynamic Theory on the Sierra Madre Occidental, Durango. The results supported the Productivity-Diversity Hypothesis, Physiological Tolerance Hypothesis and Water-Energy Dynamic Theory, but not the Mid-Domain Effect or Metabolic Theory. The annual aridity index was the variable most closely related to the diversity indices analyzed. Contemporary climate was found to have moderate to strong effects on the minimum, median and maximum tree species diversity. Because water-energy dynamics provided a satisfactory explanation for the patterns of minimum, median and maximum diversity, an understanding of this factor is critical to future biodiversity research. Quantile regression of the data showed that the three diversity parameters of tree species are generally higher in cold

Patterns of tree species diversity in relation to climatic factors on the Sierra Madre Occidental, Mexico.

PubMed

Silva-Flores, Ramón; Pérez-Verdín, Gustavo; Wehenkel, Christian

2014-01-01

Biological diversity can be defined as variability among living organisms from all sources, including terrestrial organisms, marine and other aquatic ecosystems, and the ecological complexes which they are part of. This includes diversity within species, between species, and of ecosystems. Numerous diversity indices combine richness and evenness in a single expression, and several climate-based explanations have been proposed to explain broad-scale diversity patterns. However, climate-based water-energy dynamics appears to be an essential factor that determines patterns of diversity. The Mexican Sierra Madre Occidental occupies an area of about 29 million hectares and is located between the Neotropical and Holarctic ecozones. It shelters a high diversity of flora, including 24 different species of Pinus (ca. 22% on the whole), 54 species of Quercus (ca. 9-14%), 7 species of Arbutus (ca. 50%) and many other trees species. The objectives of this study were to model how tree species diversity is related to climatic and geographic factors and stand density and to test the Metabolic Theory, Productivity-Diversity Hypothesis, Physiological Tolerance Hypothesis, Mid-Domain Effect, and the Water-Energy Dynamic Theory on the Sierra Madre Occidental, Durango. The results supported the Productivity-Diversity Hypothesis, Physiological Tolerance Hypothesis and Water-Energy Dynamic Theory, but not the Mid-Domain Effect or Metabolic Theory. The annual aridity index was the variable most closely related to the diversity indices analyzed. Contemporary climate was found to have moderate to strong effects on the minimum, median and maximum tree species diversity. Because water-energy dynamics provided a satisfactory explanation for the patterns of minimum, median and maximum diversity, an understanding of this factor is critical to future biodiversity research. Quantile regression of the data showed that the three diversity parameters of tree species are generally higher in cold

Sin Nombre Virus and Rodent Species Diversity: A Test of the Dilution and Amplification Hypotheses

PubMed Central

Clay, Christine A.; Lehmer, Erin M.; Jeor, Stephen St.; Dearing, M. Denise

2009-01-01

Background Species diversity is proposed to greatly impact the prevalence of pathogens. Two predominant hypotheses, the “Dilution Effect” and the “Amplification Effect”, predict divergent outcomes with respect to the impact of species diversity. The Dilution Effect predicts that pathogen prevalence will be negatively correlated with increased species diversity, while the Amplification Effect predicts that pathogen prevalence will be positively correlated with diversity. For many host-pathogen systems, the relationship between diversity and pathogen prevalence has not be empirically examined. Methodology/Principal Findings We tested the Dilution and Amplification Effect hypotheses by examining the prevalence of Sin Nombre virus (SNV) with respect to diversity of the nocturnal rodent community. SNV is directly transmitted primarily between deer mice (Peromyscus maniculatus). Using mark-recapture sampling in the Spring and Fall of 2003–2005, we measured SNV prevalence in deer mice at 16 landscape level sites (3.1 hectares each) that varied in rodent species diversity. We explored several mechanisms by which species diversity may affect SNV prevalence, including reduced host density, reduced host persistence, the presence of secondary reservoirs and community composition. We found a negative relationship between species diversity and SNV prevalence in deer mice, thereby supporting the Dilution Effect hypothesis. Deer mouse density and persistence were lower at sites with greater species diversity; however, only deer mouse persistence was positively correlated with SNV prevalence. Pinyon mice (P. truei) may serve as dilution agents, having a negative effect on prevalence, while kangaroo rats (Dipodomys ordii), may have a positive effect on the prevalence of SNV, perhaps through effects on deer mouse behavior. Conclusions/Significance While previous studies on host-pathogen systems have found patterns of diversity consistent with either the Dilution or

Soil phosphorus heterogeneity promotes tree species diversity and phylogenetic clustering in a tropical seasonal rainforest.

PubMed

Xu, Wumei; Ci, Xiuqin; Song, Caiyun; He, Tianhua; Zhang, Wenfu; Li, Qiaoming; Li, Jie

2016-12-01

The niche theory predicts that environmental heterogeneity and species diversity are positively correlated in tropical forests, whereas the neutral theory suggests that stochastic processes are more important in determining species diversity. This study sought to investigate the effects of soil nutrient (nitrogen and phosphorus) heterogeneity on tree species diversity in the Xishuangbanna tropical seasonal rainforest in southwestern China. Thirty-nine plots of 400 m 2 (20 × 20 m) were randomly located in the Xishuangbanna tropical seasonal rainforest. Within each plot, soil nutrient (nitrogen and phosphorus) availability and heterogeneity, tree species diversity, and community phylogenetic structure were measured. Soil phosphorus heterogeneity and tree species diversity in each plot were positively correlated, while phosphorus availability and tree species diversity were not. The trees in plots with low soil phosphorus heterogeneity were phylogenetically overdispersed, while the phylogenetic structure of trees within the plots became clustered as heterogeneity increased. Neither nitrogen availability nor its heterogeneity was correlated to tree species diversity or the phylogenetic structure of trees within the plots. The interspecific competition in the forest plots with low soil phosphorus heterogeneity could lead to an overdispersed community. However, as heterogeneity increase, more closely related species may be able to coexist together and lead to a clustered community. Our results indicate that soil phosphorus heterogeneity significantly affects tree diversity in the Xishuangbanna tropical seasonal rainforest, suggesting that deterministic processes are dominant in this tropical forest assembly.

Avian species diversity and transmission of West Nile virus in Atlanta, Georgia.

PubMed

Levine, Rebecca S; Hedeen, David L; Hedeen, Meghan W; Hamer, Gabriel L; Mead, Daniel G; Kitron, Uriel D

2017-02-03

The dilution effect is the reduction in vector-borne pathogen transmission associated with the presence of diverse potential host species, some of which are incompetent. It is popularized as the notion that increased biodiversity leads to decreased rates of disease. West Nile virus (WNV) is an endemic mosquito-borne virus in the United States that is maintained in a zoonotic cycle involving various avian host species. In Atlanta, Georgia, substantial WNV presence in the vector and host species has not translated into a high number of human cases. To determine whether a dilution effect was contributing to this reduced transmission, we characterized the host species community composition and performed WNV surveillance of hosts and vectors in urban Atlanta between 2010 and 2011. We tested the relationship between host diversity and both host seroprevalence and vector infection rates using a negative binomial generalized linear mixed model. Regardless of how we measured host diversity or whether we considered host seroprevalence and vector infection rates as predictor variables or outcome variables, we did not detect a dilution effect. Rather, we detected an amplification effect, in which increased host diversity resulted in increased seroprevalence or infection rates; this is the first empirical evidence for this effect in a mosquito-borne system. We suggest that this effect may be driven by an over-abundance of moderately- to poorly-competent host species, such as northern cardinals and members of the Mimid family, which cause optimal hosts to become rarer and present primarily in species-rich areas. Our results support the notion that dilution or amplification effects depend more on the identities of the species comprising the host community than on the absolute diversity of hosts.

Snail species diversity impacts the infection patterns of Echinostoma spp.: Examples from field collected data.

PubMed

Zimmermann, Michael R; Luth, Kyle E; Esch, Gerald W

2017-09-26

Rapid losses of biodiversity due to the changing landscape have spurred increased interest in the role of species diversity and disease risk. A leading hypothesis for the importance of biodiversity in disease reduction is the dilution effect, which suggests that increasing species diversity within a system decreases the risk of disease among the organisms inhabiting it. The role of species diversity in trematode infection was investigated using field studies from sites across the U.S. to examine the impact of snail diversity in the infection dynamics of both first and second intermediate larval stages of Echinostoma spp. parasites. The prevalence of Echinostoma spp. sporocysts/rediae infection was not affected by increases in snail diversity, but significant negative correlations in metacercariae prevalence and intensity with snail diversity were observed. Additionally, varying effectiveness of the diluting hosts was found, i.e., snail species that were incompatible first intermediate hosts for Echinostoma spp. were more successful at diluting the echinostome parasites in the focal species, while H. trivolvis, a snail species that can harbor the first intermediate larval stages, amplified infection. These findings have important implications not only on the role of species diversity in reducing disease risk, but the success of the parasites in completing their life cycles and maintaining their abundance within an aquatic system.

Influence of a dominant consumer species reverses at increased diversity.

PubMed

Brandt, Margarita; Witman, Jon D; Chiriboga, Angel I

2012-04-01

Theory and experiments indicate that changes in consumer diversity affect benthic community structure and ecosystem functioning. Although the effects of consumer diversity have been tested in the laboratory and the field, little is known about effects of consumer diversity in the subtidal zone, one of the largest marine habitats. We investigated the grazing effects of sea urchins on algal abundance and benthic community structure in a natural subtidal habitat of the Galápagos Islands. Three species of urchins (Eucidaris, Lytechinus, and Tripneustes) were manipulated in inclusion cages following a replacement design with three levels of species richness (one, two, and three species) with all possible two-species urchin combinations. Identity was the main factor accounting for changes in the percentage of substrate grazed and benthic community structure. Two out of the three two-species assemblages grazed more than expected, suggesting a richness effect, but analyses revealed that this increased grazing was due to a sampling effect of the largest and commercially valued urchin species, Tripneustes. Benthic community structure in treatments with Eucidaris, Lytechinus, and Tripneustes alone was significantly different at the end of the experiment, suggesting that resource use differentiation occurred. Communities in Tripneustes enclosures were characterized by abundant crustose coralline algae and grazed substrate, while those without it contained abundant green foliose algae (Ulva sp.). An unexpected emergent property of the system was that the most species-rich urchin assemblage underyielded, grazing less than any other assemblage with Tripneustes, effectively reversing its dominant influence observed in the two-species treatments. While further experiments are needed to discern the mechanisms of underyielding, it may be related to changing interspecific interactions as richness increases from two to three species or to density-dependent Tripneustes grazing. This

Selection of multiple umbrella species for functional and taxonomic diversity to represent urban biodiversity.

PubMed

Sattler, T; Pezzatti, G B; Nobis, M P; Obrist, M K; Roth, T; Moretti, M

2014-04-01

Surrogates, such as umbrella species, are commonly used to reduce the complexity of quantifying biodiversity for conservation purposes. The presence of umbrella species is often indicative of high taxonomic diversity; however, functional diversity is now recognized as an important metric for biodiversity and thus should be considered when choosing umbrella species. We identified umbrella species associated with high taxonomic and functional biodiversity in urban areas in Switzerland. We analyzed 39,752 individuals of 574 animal species from 96 study plots and 1397 presences of 262 plant species from 58 plots. Thirty-one biodiversity measures of 7 taxonomic groups (plants, spiders, bees, ground beetles, lady bugs, weevils and birds) were included in within- and across-taxa analyses. Sixteen measures were taxonomical (species richness and species diversity), whereas 15 were functional (species traits including mobility, resource use, and reproduction). We used indicator value analysis to identify umbrella species associated with single or multiple biodiversity measures. Many umbrella species were indicators of high biodiversity within their own taxonomic group (from 33.3% in weevils to 93.8% in birds), to a lesser extent they were indicators across taxa. Principal component analysis revealed that umbrella species for multiple measures of biodiversity represented different aspects of biodiversity, especially with respect to measures of taxonomic and functional diversity. Thus, even umbrella species for multiple measures of biodiversity were complementary in the biodiversity aspects they represented. Thus, the choice of umbrella species based solely on taxonomic diversity is questionable and may not represent biodiversity comprehensively. Our results suggest that, depending on conservation priorities, managers should choose multiple and complementary umbrella species to assess the state of biodiversity. © 2013 Society for Conservation Biology.

Colitis and Colon Cancer in WASP-Deficient Mice Require Helicobacter Spp.

PubMed Central

Nguyen, Deanna D.; Muthupalani, Suresh; Goettel, Jeremy A.; Eston, Michelle A.; Mobley, Melissa; Taylor, Nancy S.; McCabe, Amanda; Marin, Romela; Snapper, Scott B.; Fox, James G.

2014-01-01

Background Wiskott-Aldrich Syndrome protein (WASP)-deficient patients and mice are immunodeficient and can develop inflammatory bowel disease. The intestinal microbiome is critical to the development of colitis in most animal models, in which, Helicobacter spp. have been implicated in disease pathogenesis. We sought to determine the role of Helicobacter spp. in colitis development in WASP-deficient (WKO) mice. Methods Feces from WKO mice raised under specific pathogen free conditions were evaluated for the presence of Helicobacter spp., after which, a subset of mice were rederived in Helicobacter spp.-free conditions. Helicobacter spp.-free WKO animals were subsequently infected with Helicobacter bilis. Results Helicobacter spp. were detected in feces from WKO mice. After re-derivation in Helicobacter spp.-free conditions, WKO mice did not develop spontaneous colitis but were susceptible to radiation-induced colitis. Moreover, a T-cell transfer model of colitis dependent on WASP-deficient innate immune cells also required Helicobacter spp. colonization. Helicobacter bilis infection of rederived WKO mice led to typhlitis and colitis. Most notably, several H. bilis-infected animals developed dysplasia with 10% demonstrating colon carcinoma, which was not observed in uninfected controls. Conclusions Spontaneous and T-cell transfer, but not radiation-induced, colitis in WKO mice is dependent on the presence of Helicobacter spp. Furthermore, H. bilis infection is sufficient to induce typhlocolitis and colon cancer in Helicobacter spp.-free WKO mice. This animal model of a human immunodeficiency with chronic colitis and increased risk of colon cancer parallels what is seen in human colitis and implicates specific microbial constituents in promoting immune dysregulation in the intestinal mucosa. PMID:23820270

Does species diversity limit productivity in natural grassland communities?

USGS Publications Warehouse

Grace, J.B.; Anderson, T.M.; Smith, M.D.; Seabloom, E.; Andelman, S.J.; Meche, G.; Weiher, E.; Allain, L.K.; Jutila, H.; Sankaran, M.; Knops, J.; Ritchie, M.; Willig, M.R.

2007-01-01

Theoretical analyses and experimental studies of synthesized assemblages indicate that under particular circumstances species diversity can enhance community productivity through niche complementarity. It remains unclear whether this process has important effects in mature natural ecosystems where competitive feedbacks and complex environmental influences affect diversity-productivity relationships. In this study, we evaluated diversity-productivity relationships while statistically controlling for environmental influences in 12 natural grassland ecosystems. Because diversity-productivity relationships are conspicuously nonlinear, we developed a nonlinear structural equation modeling (SEM) methodology to separate the effects of diversity on productivity from the effects of productivity on diversity. Meta-analysis was used to summarize the SEM findings across studies. While competitive effects were readily detected, enhancement of production by diversity was not. These results suggest that the influence of small-scale diversity on productivity in mature natural systems is a weak force, both in absolute terms and relative to the effects of other controls on productivity. ?? 2007 Blackwell Publishing Ltd/CNRS.

Genetic diversity among and within cultured cyanobionts of diverse species of Azolla.

PubMed

Sood, A; Prasanna, R; Prasanna, B M; Singh, P K

2008-01-01

The cyanobionts isolated from 10 Azolla accessions belonging to 6 species (Azolla mexicana, A. microphylla, A. rubra, A. caroliniana, A. filiculoides, A. pinnata) were cultured under laboratory conditions and analyzed on the basis of whole cell protein profiles and molecular marker dataset generated using repeat sequence primers (STRR(mod) and HipTG). The biochemical and molecular marker profiles of the cyanobionts were compared with those of the free-living cyanobacteria and symbiotic Nostoc strains from Anthoceros sp., Cycas sp. and Gunnera monoika. Cluster analysis revealed the genetic diversity among the selected strains, and identified 3 distinct clusters. Group 1 included cyanobionts from all the 10 accessions of Azolla, group 2 comprised all the symbiotic Nostoc strains, while group 3 included the free-living cyanobacteria belonging to the genera Nostoc and Anabaena. The interrelationships among the Azolla cyanobionts were further revealed by principal component analysis. Cyanobionts from A. caroliniana-A. microphylla grouped together while cyanobionts associated with A. mexicana-A. filiculoides along with A. pinnata formed another group. A. rubra cyanobionts had intermediate relationship with both the subgroups. This is the first study analyzing the diversity existing among the cultured cyanobionts of diverse Azolla species through the use of biochemical and molecular profiles and also the genetic distinctness of these free-living cyanobionts as compared to cyanobacterial strains of the genera Anabaena and Nostoc.

Helicobacter pylori oipA, vacA and dupA genetic diversity in individual hosts.

PubMed

Matteo, Mario José; Armitano, Rita Inés; Granados, Gabriela; Wonaga, Andrés Dario; Sánches, Christian; Olmos, Martín; Catalano, Mariana

2010-01-01

Helicobacter pylori putative virulence factors can undergo a continuously evolving mechanism as an approach to bacterial adaptation to the host changing environment during chronic infection. oipA, vacA and dupA genetic diversity among isolates from multiple biopsies (niches) from the antrum and corpus of 40 patients was investigated. A set of 229 isolates was examined. Direct DNA sequence analysis of amplified fragments was used to study oipA 'on/off' expression status as well as the presence of C or T insertion in jhp0917 that originates a continuous (jhp0917-jhp0918) dupA gene. vacA alleles were identified by multiplex PCR. Different inter-niches oipA CT repeat patterns were observed in nine patients; in six of these, 'on' and 'off' mixed patterns were found. In three of these nine patients, different vacA alleles were also observed in a single host. Inter-niche dupA differences involved the absence and presence of jhp0917 and/or jhp0918 or mutations in dupA, including those that may originate a non-functional gene, and they were also present in two patients with mixed oipA CT patterns and in another seven patients. Evidence of mixed infection was observed in two patients only. In conclusion, oipA and dupA genes showed similar inter-niche variability, occurring in approximately 1/4 patients. Conversely, vacA allele microevolution seemed to be a less common event, occurring in approximately 1/10 patients, probably due to the mechanism that this gene evolves 'in vivo'.

Deciphering the enigma of undetected species, phylogenetic, and functional diversity based on Good-Turing theory.

PubMed

Chao, Anne; Chiu, Chun-Huo; Colwell, Robert K; Magnago, Luiz Fernando S; Chazdon, Robin L; Gotelli, Nicholas J

2017-11-01

Estimating the species, phylogenetic, and functional diversity of a community is challenging because rare species are often undetected, even with intensive sampling. The Good-Turing frequency formula, originally developed for cryptography, estimates in an ecological context the true frequencies of rare species in a single assemblage based on an incomplete sample of individuals. Until now, this formula has never been used to estimate undetected species, phylogenetic, and functional diversity. Here, we first generalize the Good-Turing formula to incomplete sampling of two assemblages. The original formula and its two-assemblage generalization provide a novel and unified approach to notation, terminology, and estimation of undetected biological diversity. For species richness, the Good-Turing framework offers an intuitive way to derive the non-parametric estimators of the undetected species richness in a single assemblage, and of the undetected species shared between two assemblages. For phylogenetic diversity, the unified approach leads to an estimator of the undetected Faith's phylogenetic diversity (PD, the total length of undetected branches of a phylogenetic tree connecting all species), as well as a new estimator of undetected PD shared between two phylogenetic trees. For functional diversity based on species traits, the unified approach yields a new estimator of undetected Walker et al.'s functional attribute diversity (FAD, the total species-pairwise functional distance) in a single assemblage, as well as a new estimator of undetected FAD shared between two assemblages. Although some of the resulting estimators have been previously published (but derived with traditional mathematical inequalities), all taxonomic, phylogenetic, and functional diversity estimators are now derived under the same framework. All the derived estimators are theoretically lower bounds of the corresponding undetected diversities; our approach reveals the sufficient conditions under

Beyond 16S rRNA Community Profiling: Intra-Species Diversity in the Gut Microbiota

PubMed Central

Ellegaard, Kirsten M.; Engel, Philipp

2016-01-01

Interactions with microbes affect many aspects of animal biology, including immune system development, nutrition and health. In vertebrates, the gut microbiota is dominated by a small subset of phyla, but the species composition within these phyla is typically not conserved. Moreover, several recent studies have shown that bacterial species in the gut are composed of a multitude of strains, which frequently co-exist in their host, and may be host-specific. However, since the study of intra-species diversity is challenging, particularly in the setting of complex, host-associated microbial communities, our current understanding of the distribution, evolution and functional relevance of intra-species diversity in the gut is scarce. In order to unravel how genomic diversity translates into phenotypic diversity, community analyses going beyond 16S rRNA profiling, in combination with experimental approaches, are needed. Recently, the honeybee has emerged as a promising model for studying gut bacterial communities, particularly in terms of strain-level diversity. Unlike most other invertebrates, the honeybee gut is colonized by a remarkably consistent and specific core microbiota, which is dominated by only eight bacterial species. As for the vertebrate gut microbiota, these species are composed of highly diverse strains suggesting that similar evolutionary forces shape gut community structures in vertebrates and social insects. In this review, we outline current knowledge on the evolution and functional relevance of strain diversity within the gut microbiota, including recent insights gained from mammals and other animals such as the honeybee. We discuss methodological approaches and propose possible future avenues for studying strain diversity in complex bacterial communities. PMID:27708630

Beyond 16S rRNA Community Profiling: Intra-Species Diversity in the Gut Microbiota.

PubMed

Ellegaard, Kirsten M; Engel, Philipp

2016-01-01

Interactions with microbes affect many aspects of animal biology, including immune system development, nutrition and health. In vertebrates, the gut microbiota is dominated by a small subset of phyla, but the species composition within these phyla is typically not conserved. Moreover, several recent studies have shown that bacterial species in the gut are composed of a multitude of strains, which frequently co-exist in their host, and may be host-specific. However, since the study of intra-species diversity is challenging, particularly in the setting of complex, host-associated microbial communities, our current understanding of the distribution, evolution and functional relevance of intra-species diversity in the gut is scarce. In order to unravel how genomic diversity translates into phenotypic diversity, community analyses going beyond 16S rRNA profiling, in combination with experimental approaches, are needed. Recently, the honeybee has emerged as a promising model for studying gut bacterial communities, particularly in terms of strain-level diversity. Unlike most other invertebrates, the honeybee gut is colonized by a remarkably consistent and specific core microbiota, which is dominated by only eight bacterial species. As for the vertebrate gut microbiota, these species are composed of highly diverse strains suggesting that similar evolutionary forces shape gut community structures in vertebrates and social insects. In this review, we outline current knowledge on the evolution and functional relevance of strain diversity within the gut microbiota, including recent insights gained from mammals and other animals such as the honeybee. We discuss methodological approaches and propose possible future avenues for studying strain diversity in complex bacterial communities.

Habitat Heterogeneity Affects Plant and Arthropod Species Diversity and Turnover in Traditional Cornfields

PubMed Central

Martínez, Eliana; Rös, Matthias; Bonilla, María Argenis; Dirzo, Rodolfo

2015-01-01

The expansion of the agricultural frontier by the clearing of remnant forests has led to human-dominated landscape mosaics. Previous studies have evaluated the effect of these landscape mosaics on arthropod diversity at local spatial scales in temperate and tropical regions, but little is known about fragmentation effects in crop systems, such as the complex tropical traditional crop systems that maintain a high diversity of weeds and arthropods in low-Andean regions. To understand the factors that influence patterns of diversity in human-dominated landscapes, we investigate the effect of land use types on plant and arthropod diversity in traditionally managed cornfields, via surveys of plants and arthropods in twelve traditional cornfields in the Colombian Andes. We estimated alpha and beta diversity to analyze changes in diversity related to land uses within a radius of 100 m to 1 km around each cornfield. We observed that forests influenced alpha diversity of plants, but not of arthropods. Agricultural lands had a positive relationship with plants and herbivores, but a negative relationship with predators. Pastures positively influenced the diversity of plants and arthropods. In addition, forest cover seemed to influence changes in plant species composition and species turnover of herbivore communities among cornfields. The dominant plant species varied among fields, resulting in high differentiation of plant communities. Predator communities also exhibited high turnover among cornfields, but differences in composition arose mainly among rare species. The crop system evaluated in this study represents a widespread situation in the tropics, therefore, our results can be of broad significance. Our findings suggest that traditional agriculture may not homogenize biological communities, but instead could maintain the regional pool of species through high beta diversity. PMID:26197473

Drought responses by individual tree species are not often correlated with tree species diversity in European forests

DOE PAGES

Forrester, David I.; Bonal, Damien; Dawud, Seid; ...

2016-07-26

Drought frequency and intensity are predicted to increase in many parts of the Northern Hemisphere and the effects of such changes on forest growth and tree mortality are already evident in many regions around the world. Mixed-species forests and increasing tree species diversity have been put forward as important risk reduction and adaptation strategies in the face of climate change. But, little is known about whether the species interactions that occur in diverse forests will reduce drought susceptibility or water stress. In this study, we focused on the effect of drought on individual tree species (n = 16) within sixmore » regions of Europe and assessed whether this response was related to tree species diversity and stand density, and whether community-level responses resulted from many similar or contrasting species-level responses. For each species in each plot, we calculated the increase in carbon isotope composition of latewood from a wet to a dry year (Δδ13C) as an estimate of its drought stress level. Furthermore, when significant community-level relationships occurred (three of six regions), there was only one species within the given community that showed a significant relationship (three of 25 species–region combinations), showing that information about a single species can be a poor indicator of the response of other species or the whole community. There were many two-species mixtures in which both species were less water-stressed compared with their monocultures, but also many mixtures where both species were more stressed compared with their monocultures. Furthermore, a given species combination responded differently in different regions. Synthesis and applications. Our study shows that drought stress may sometimes be reduced in mixed-species forests, but this is not a general pattern, and even varies between sites for a given combination. The management or prediction of drought stress requires consideration of the physiological characteristics

Drought responses by individual tree species are not often correlated with tree species diversity in European forests

DOE Office of Scientific and Technical Information (OSTI.GOV)

Forrester, David I.; Bonal, Damien; Dawud, Seid

Drought frequency and intensity are predicted to increase in many parts of the Northern Hemisphere and the effects of such changes on forest growth and tree mortality are already evident in many regions around the world. Mixed-species forests and increasing tree species diversity have been put forward as important risk reduction and adaptation strategies in the face of climate change. But, little is known about whether the species interactions that occur in diverse forests will reduce drought susceptibility or water stress. In this study, we focused on the effect of drought on individual tree species (n = 16) within sixmore » regions of Europe and assessed whether this response was related to tree species diversity and stand density, and whether community-level responses resulted from many similar or contrasting species-level responses. For each species in each plot, we calculated the increase in carbon isotope composition of latewood from a wet to a dry year (Δδ13C) as an estimate of its drought stress level. Furthermore, when significant community-level relationships occurred (three of six regions), there was only one species within the given community that showed a significant relationship (three of 25 species–region combinations), showing that information about a single species can be a poor indicator of the response of other species or the whole community. There were many two-species mixtures in which both species were less water-stressed compared with their monocultures, but also many mixtures where both species were more stressed compared with their monocultures. Furthermore, a given species combination responded differently in different regions. Synthesis and applications. Our study shows that drought stress may sometimes be reduced in mixed-species forests, but this is not a general pattern, and even varies between sites for a given combination. The management or prediction of drought stress requires consideration of the physiological characteristics

Criterion 1: Conservation of biological diversity - Indicator 9: Population levels of representative species from diverse habitats monitored across their range

Treesearch

Carolyn Hull Sieg; Curtis H. Flather; Noah Barstatis

2003-01-01

This indicator estimates population trends of selected species as a surrogate measure of genetic diversity. Decreases in genetic diversity as populations decline, particularly if associated with small populations, contribute to increased risk of extinction. This indicator also provides an important measure of general biodiversity, as changes in species abundances are a...

Consumer species richness and nutrients interact in determining producer diversity.

PubMed

Groendahl, Sophie; Fink, Patrick

2017-03-17

While it is crucial to understand the factors that determine the biodiversity of primary producer communities, the relative importance of bottom-up and top-down control factors is still poorly understood. Using freshwater benthic algal communities in the laboratory as a model system, we find an unimodal relationship between nutrient availability and producer diversity, and that increasing number of consumer species increases producer diversity, but overall grazing decreases algal biodiversity. Interestingly, these two factors interact strongly in determining producer diversity, as an increase in nutrient supply diminishes the positive effect of consumer species richness on producer biodiversity. This novel and thus-far overlooked interaction of bottom-up and top-down control mechanisms of biodiversity may have a pronounced impact on ecosystem functioning and thus have repercussions for the fields of biodiversity conservation and restoration.

HELICOBACTER PYLORI

EPA Science Inventory

Helicobacter pylori is a pathogenic bacteria which inhabits the human stomach and upper gastrointestinal tract. This encyclopedic entry summarizes the potential role of this organism as a waterborne pathogen. Information is provided on the physiology and morphology of this bacter...

Species diversity of ectoparasitic chigger mites (Acari: Prostigmata) on small mammals in Yunnan Province, China.

PubMed

Peng, Pei-Ying; Guo, Xian-Guo; Ren, Tian-Guang; Song, Wen-Yu; Dong, Wen-Ge; Fan, Rong

2016-09-01

Chigger mites are a large group of arthropods and the larvae of mites are ectoparasites. Some species of ectoparasitic mites (larvae) can be the transmitting vectors of tsutsugamushi disease (scrub typhus). Yunnan Province is located in the southwest of China with complicated topographic landform and high biodiversity, where there are five zoogeographical subregions. Rodents and some other small mammals were trapped and examined for ectoparasitic chigger mites in 29 investigation sites in Yunnan during 2001-2013. From 13,760 individuals and 76 species of small mammal hosts, we collected 274 species of mites, which were identified as comprising 26 genera in two families. The species diversity of chigger mites (274 species) in the present study were not only much higher than that from other provinces of China but also largely exceeded that recorded from other regions and countries in the world. Of the five zoogeographical subregions, both the species diversity and Shannon-Weiner's diversity of mites were the highest in subregion II (southern subregion of Hengduan Mountains) with middle altitudes and middle latitude. Both the species diversity of mites and Shannon-Wiener diversity index showed a parabolic tendency from the low altitude (<500 m) to the high altitude (>3500 m) along the vertical gradients with the peak occurring in the middle-altitude regions (2000-2500 m). Of four dominant hosts, the species richness of mites was highest on Eothenomys miletus (S = 165) and Shannon-Wiener diversity index was highest on Rattus norvegicus (H = 3.13). Along latitude gradients, species richness of chigger mites increased first and then decreased, peaking at 25° to 26° N with 193 mite species. The geographical location, complex topography, and landscape with diverse small mammal hosts in Yunnan Province have contributed to the extremely high species diversity of mites in the province. The large sampling size of small mammal hosts in a wide geographical scope

Antibiotics reduce genetic diversity of core species in the honeybee gut microbiome.

PubMed

Raymann, Kasie; Bobay, Louis-Marie; Moran, Nancy A

2018-04-01

The gut microbiome plays a key role in animal health, and perturbing it can have detrimental effects. One major source of perturbation to microbiomes, in humans and human-associated animals, is exposure to antibiotics. Most studies of how antibiotics affect the microbiome have used amplicon sequencing of highly conserved 16S rRNA sequences, as in a recent study showing that antibiotic treatment severely alters the species-level composition of the honeybee gut microbiome. But because the standard 16S rRNA-based methods cannot resolve closely related strains, strain-level changes could not be evaluated. To address this gap, we used amplicon sequencing of protein-coding genes to assess effects of antibiotics on fine-scale genetic diversity of the honeybee gut microbiota. We followed the population dynamics of alleles within two dominant core species of the bee gut community, Gilliamella apicola and Snodgrassella alvi, following antibiotic perturbation. Whereas we observed a large reduction in genetic diversity in G. apicola, S. alvi diversity was mostly unaffected. The reduction in G. apicola diversity accompanied an increase in the frequency of several alleles, suggesting resistance to antibiotic treatment. We find that antibiotic perturbation can cause major shifts in diversity and that the extent of these shifts can vary substantially across species. Thus, antibiotics impact not only species composition, but also allelic diversity within species, potentially affecting hosts if variants with particular functions are reduced or eliminated. Overall, we show that amplicon sequencing of protein-coding genes, without clustering into operational taxonomic units, provides an accurate picture of the fine-scale dynamics of microbial communities over time. © 2017 John Wiley & Sons Ltd.

Toward a trophic theory of species diversity

PubMed Central

Terborgh, John W.

2015-01-01

Efforts to understand the ecological regulation of species diversity via bottom-up approaches have failed to yield a consensus theory. Theories based on the alternative of top-down regulation have fared better. Paine’s discovery of keystone predation demonstrated that the regulation of diversity via top-down forcing could be simple, strong, and direct, yet ecologists have persistently failed to perceive generality in Paine’s result. Removing top predators destabilizes many systems and drives transitions to radically distinct alternative states. These transitions typically involve community reorganization and loss of diversity, implying that top-down forcing is crucial to diversity maintenance. Contrary to the expectations of bottom-up theories, many terrestrial herbivores and mesopredators are capable of sustained order-of-magnitude population increases following release from predation, negating the assumption that populations of primary consumers are resource limited and at or near carrying capacity. Predation sensu lato (to include Janzen–Connell mortality agents) has been shown to promote diversity in a wide range of ecosystems, including rocky intertidal shelves, coral reefs, the nearshore ocean, streams, lakes, temperate and tropical forests, and arctic tundra. The compelling variety of these ecosystems suggests that top-down forcing plays a universal role in regulating diversity. This conclusion is further supported by studies showing that the reduction or absence of predation leads to diversity loss and, in the more dramatic cases, to catastrophic regime change. Here, I expand on the thesis that diversity is maintained by the interaction between predation and competition, such that strong top-down forcing reduces competition, allowing coexistence. PMID:26374788

A neutral theory for interpreting correlations between species and genetic diversity in communities.

PubMed

Laroche, Fabien; Jarne, Philippe; Lamy, Thomas; David, Patrice; Massol, Francois

2015-01-01

Spatial patterns of biological diversity have been extensively studied in ecology and population genetics, because they reflect the forces acting on biodiversity. A growing number of studies have found that genetic (within-species) and species diversity can be correlated in space (the so-called species-gene diversity correlation [SGDC]), which suggests that they are controlled by nonindependent processes. Positive SGDCs are generally assumed to arise from parallel responses of genetic and species diversity to variation in site size and connectivity. However, this argument implicitly assumes a neutral model that has yet to be developed. Here, we build such a model to predict SGDC in a metacommunity. We describe how SGDC emerges from competition within sites and variation in connectivity and carrying capacity among sites. We then introduce the formerly ignored mutation process, which affects genetic but not species diversity. When mutation rate is low, our model confirms that variation in the number of migrants among sites creates positive SGDCs. However, when considering high mutation rates, interactions between mutation, migration, and competition can produce negative SGDCs. Neutral processes thus do not always contribute positively to SGDCs. Our approach provides empirical guidelines for interpreting these novel patterns in natura with respect to evolutionary and ecological forces shaping metacommunities.

Correlating Species and Spectral Diversity using Remote Sensing in Successional Fields in Virginia

NASA Astrophysics Data System (ADS)

Aneece, I.; Epstein, H. E.

2015-12-01

Conserving biodiversity can help preserve ecosystem properties and function. As the increasing prevalence of invasive plant species threatens biodiversity, advances in remote sensing technology can help monitor invasive species and their effects on ecosystems and plant communities. To assess whether we could study the effects of invasive species on biodiversity using remote sensing, we asked whether species diversity was positively correlated with spectral diversity, and whether correlations differed among spectral regions along the visible and near-infrared range. To answer these questions, we established community plots in secondary successional fields at the Blandy Experimental Farm in northern Virginia and collected vegetation surveys and ground-level hyperspectral data from 350 to 1025 nm wavelengths. Pearson correlation analysis revealed a positive correlation between spectral diversity and species diversity in the visible ranges of 350-499 nm (Pearson correlation=0.69, p=0.01), 500-589 nm (Pearson=0.64, p=0.03), and 590-674 nm (Pearson=0.70, p=0.01), slight positive correlation in the red edge range of 675-754 nm (Pearson=0.56, p=0.06), and no correlation in the near-infrared ranges of 755-924 nm (Pearson=-0.06, p=0.85) and 925-1025 nm (Pearson=0.30, p=0.34). These differences in correlations across spectral regions may be due to the elements that contribute to signatures in those regions and spectral data transformation methods. To investigate the role of pigment variability in these correlations, we estimated chlorophyll, carotenoid, and anthocyanin concentrations of five dominant species in the plots using vegetation indices. Although interspecific variability in pigment levels exceeded intraspecific variability, chlorophyll (F value=118) was more varied within species than carotenoids (F=322) and anthocyanins (F=126), perhaps contributing to the lack of correlation between species diversity and spectral diversity in the red edge region. Interspecific

Operational Tree Species Mapping in a Diverse Tropical Forest with Airborne Imaging Spectroscopy.

PubMed

Baldeck, Claire A; Asner, Gregory P; Martin, Robin E; Anderson, Christopher B; Knapp, David E; Kellner, James R; Wright, S Joseph

2015-01-01

Remote identification and mapping of canopy tree species can contribute valuable information towards our understanding of ecosystem biodiversity and function over large spatial scales. However, the extreme challenges posed by highly diverse, closed-canopy tropical forests have prevented automated remote species mapping of non-flowering tree crowns in these ecosystems. We set out to identify individuals of three focal canopy tree species amongst a diverse background of tree and liana species on Barro Colorado Island, Panama, using airborne imaging spectroscopy data. First, we compared two leading single-class classification methods--binary support vector machine (SVM) and biased SVM--for their performance in identifying pixels of a single focal species. From this comparison we determined that biased SVM was more precise and created a multi-species classification model by combining the three biased SVM models. This model was applied to the imagery to identify pixels belonging to the three focal species and the prediction results were then processed to create a map of focal species crown objects. Crown-level cross-validation of the training data indicated that the multi-species classification model had pixel-level producer's accuracies of 94-97% for the three focal species, and field validation of the predicted crown objects indicated that these had user's accuracies of 94-100%. Our results demonstrate the ability of high spatial and spectral resolution remote sensing to accurately detect non-flowering crowns of focal species within a diverse tropical forest. We attribute the success of our model to recent classification and mapping techniques adapted to species detection in diverse closed-canopy forests, which can pave the way for remote species mapping in a wider variety of ecosystems.

Tree diversity and the role of non-host neighbour tree species in reducing fungal pathogen infestation

PubMed Central

Hantsch, Lydia; Bien, Steffen; Radatz, Stine; Braun, Uwe; Auge, Harald; Bruelheide, Helge

2014-01-01

The degree to which plant pathogen infestation occurs in a host plant is expected to be strongly influenced by the level of species diversity among neighbouring host and non-host plant species. Since pathogen infestation can negatively affect host plant performance, it can mediate the effects of local biodiversity on ecosystem functioning. We tested the effects of tree diversity and the proportion of neighbouring host and non-host species with respect to the foliar fungal pathogens of Tilia cordata and Quercus petraea in the Kreinitz tree diversity experiment in Germany. We hypothesized that fungal pathogen richness increases while infestation decreases with increasing local tree diversity. In addition, we tested whether fungal pathogen richness and infestation are dependent on the proportion of host plant species present or on the proportion of particular non-host neighbouring tree species. Leaves of the two target species were sampled across three consecutive years with visible foliar fungal pathogens on the leaf surface being identified macro- and microscopically. Effects of diversity among neighbouring trees were analysed: (i) for total fungal species richness and fungal infestation on host trees and (ii) for infestation by individual fungal species. We detected four and five fungal species on T. cordata and Q. petraea, respectively. High local tree diversity reduced (i) total fungal species richness and infestation of T. cordata and fungal infestation of Q. petraea and (ii) infestation by three host-specialized fungal pathogen species. These effects were brought about by local tree diversity and were independent of host species proportion. In general, host species proportion had almost no effect on fungal species richness and infestation. Strong effects associated with the proportion of particular non-host neighbouring tree species on fungal species richness and infestation were, however, recorded. Synthesis. For the first time, we experimentally

Tree diversity and the role of non-host neighbour tree species in reducing fungal pathogen infestation.

PubMed

Hantsch, Lydia; Bien, Steffen; Radatz, Stine; Braun, Uwe; Auge, Harald; Bruelheide, Helge

2014-11-01

The degree to which plant pathogen infestation occurs in a host plant is expected to be strongly influenced by the level of species diversity among neighbouring host and non-host plant species. Since pathogen infestation can negatively affect host plant performance, it can mediate the effects of local biodiversity on ecosystem functioning.We tested the effects of tree diversity and the proportion of neighbouring host and non-host species with respect to the foliar fungal pathogens of Tilia cordata and Quercus petraea in the Kreinitz tree diversity experiment in Germany. We hypothesized that fungal pathogen richness increases while infestation decreases with increasing local tree diversity. In addition, we tested whether fungal pathogen richness and infestation are dependent on the proportion of host plant species present or on the proportion of particular non-host neighbouring tree species.Leaves of the two target species were sampled across three consecutive years with visible foliar fungal pathogens on the leaf surface being identified macro- and microscopically. Effects of diversity among neighbouring trees were analysed: (i) for total fungal species richness and fungal infestation on host trees and (ii) for infestation by individual fungal species.We detected four and five fungal species on T. cordata and Q. petraea , respectively. High local tree diversity reduced (i) total fungal species richness and infestation of T. cordata and fungal infestation of Q. petraea and (ii) infestation by three host-specialized fungal pathogen species. These effects were brought about by local tree diversity and were independent of host species proportion. In general, host species proportion had almost no effect on fungal species richness and infestation. Strong effects associated with the proportion of particular non-host neighbouring tree species on fungal species richness and infestation were, however, recorded. Synthesis . For the first time, we experimentally

Legume Diversity Patterns in West Central Africa: Influence of Species Biology on Distribution Models

PubMed Central

de la Estrella, Manuel; Mateo, Rubén G.; Wieringa, Jan J.; Mackinder, Barbara; Muñoz, Jesús

2012-01-01

Objectives Species Distribution Models (SDMs) are used to produce predictions of potential Leguminosae diversity in West Central Africa. Those predictions are evaluated subsequently using expert opinion. The established methodology of combining all SDMs is refined to assess species diversity within five defined vegetation types. Potential species diversity is thus predicted for each vegetation type respectively. The primary aim of the new methodology is to define, in more detail, areas of species richness for conservation planning. Methodology Using Maxent, SDMs based on a suite of 14 environmental predictors were generated for 185 West Central African Leguminosae species, each categorised according to one of five vegetation types: Afromontane, coastal, non-flooded forest, open formations, or riverine forest. The relative contribution of each environmental variable was compared between different vegetation types using a nonparametric Kruskal-Wallis analysis followed by a post-hoc Kruskal-Wallis Paired Comparison contrast. Legume species diversity patterns were explored initially using the typical method of stacking all SDMs. Subsequently, five different ensemble models were generated by partitioning SDMs according to vegetation category. Ecological modelers worked with legume specialists to improve data integrity and integrate expert opinion in the interpretation of individual species models and potential species richness predictions for different vegetation types. Results/Conclusions Of the 14 environmental predictors used, five showed no difference in their relative contribution to the different vegetation models. Of the nine discriminating variables, the majority were related to temperature variation. The set of variables that played a major role in the Afromontane species diversity model differed significantly from the sets of variables of greatest relative important in other vegetation categories. The traditional approach of stacking all SDMs indicated overall

Helicobacter cinaedi bacteremia with cellulitis after ABO-incompatible living-donor liver transplantation: Case report.

PubMed

Mishima, Kohei; Obara, Hideaki; Sugita, Kayoko; Shinoda, Masahiro; Kitago, Minoru; Abe, Yuta; Hibi, Taizo; Yagi, Hiroshi; Matsubara, Kentaro; Mori, Takehiko; Takano, Yaoko; Fujiwara, Hiroshi; Itano, Osamu; Hasegawa, Naoki; Iwata, Satoshi; Kitagawa, Yuko

2015-07-07

Helicobacter cinaedi (H. cinaedi), a Gram-negative spiral-shaped bacterium, is an enterohepatic non-Helicobacter pylori Helicobacter species. We report the first case of H. cinaedi bacteremia with cellulitis after liver transplantation. A 48-year-old male, who had been a dog breeder for 15 years, underwent ABO-incompatible living-donor liver transplantation for hepatitis C virus-induced decompensated cirrhosis using an anti-hepatitis B core antibody-positive graft. The patient was preoperatively administered rituximab and underwent plasma exchange twice to overcome blood type incompatibility. After discharge, he had been doing well with immunosuppression therapy comprising cyclosporine, mycophenolate mofetil, and steroid according to the ABO-incompatible protocol of our institution. However, 7 mo after transplantation, he was admitted to our hospital with a diagnosis of recurrent cellulitis on the left lower extremity, and H. cinaedi was detected by both blood culture and polymerase chain reaction analysis. Antibiotics improved his symptoms, and he was discharged at day 30 after admission. Clinicians should be more aware of H. cinaedi in immunocompromised patients, such as ABO-incompatible transplant recipients.

Genetic variation of loci potentially under selection confounds species-genetic diversity correlations in a fragmented habitat.

PubMed

Bertin, Angeline; Gouin, Nicolas; Baumel, Alex; Gianoli, Ernesto; Serratosa, Juan; Osorio, Rodomiro; Manel, Stephanie

2017-01-01

Positive species-genetic diversity correlations (SGDCs) are often thought to result from the parallel influence of neutral processes on genetic and species diversity. Yet, confounding effects of non-neutral mechanisms have not been explored. Here, we investigate the impact of non-neutral genetic diversity on SGDCs in high Andean wetlands. We compare correlations between plant species diversity and genetic diversity (GD) calculated with and without loci potentially under selection (outlier loci). The study system includes 2188 specimens from five species (three common aquatic macroinvertebrate and two dominant plant species) that were genotyped for 396 amplified fragment length polymorphism loci. We also appraise the importance of neutral processes on SGDCs by investigating the influence of habitat fragmentation features. Significant positive SGDCs were detected for all five species (mean SGDC = 0.52 ± 0.05). While only a few outlier loci were detected in each species, they resulted in significant decreases in GD and in SGDCs. This supports the hypothesis that neutral processes drive species-genetic diversity relationships in high Andean wetlands. Unexpectedly, the effects on genetic diversity GD of the habitat fragmentation characteristics in this study increased with the presence of outlier loci in two species. Overall, our results reveal pitfalls in using habitat features to infer processes driving SGDCs and show that a few loci potentially under selection are enough to cause a significant downward bias in SGDC. Investigating confounding effects of outlier loci thus represents a useful approach to evidence the contribution of neutral processes on species-genetic diversity relationships. © 2016 John Wiley & Sons Ltd.

High genetic diversity in the endangered and narrowly distributed amphibian species Leptobrachium leishanense.

PubMed

Zhang, Wei; Luo, Zhenhua; Zhao, Mian; Wu, Hua

2015-09-01

Threatened species typically have a small or declining population size, which make them highly susceptible to loss of genetic diversity through genetic drift and inbreeding. Genetic diversity determines the evolutionary potential of a species; therefore, maintaining the genetic diversity of threatened species is essential for their conservation. In this study, we assessed the genetic diversity of the adaptive major histocompatibility complex (MHC) genes in an endangered and narrowly distributed amphibian species, Leptobrachium leishanense in Southwest China. We compared the genetic variation of MHC class I genes with that observed in neutral markers (5 microsatellite loci and cytochrome b gene) to elucidate the relative roles of genetic drift and natural selection in shaping the current MHC polymorphism in this species. We found a high level of genetic diversity in this population at both MHC and neutral markers compared with other threatened amphibian species. Historical positive selection was evident in the MHC class I genes. The higher allelic richness in MHC markers compared with that of microsatellite loci suggests that selection rather than genetic drift plays a prominent role in shaping the MHC variation pattern, as drift can affect all the genome in a similar way but selection directly targets MHC genes. Although demographic analysis revealed no recent bottleneck events in L. leishanense, additional population decline will accelerate the dangerous status for this species. We suggest that the conservation management of L. leishanense should concentrate on maximizing the retention of genetic diversity through preventing their continuous population decline. Protecting their living habitats and forbidding illegal hunting are the most important measures for conservation of L. leishanense. © 2015 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and Wiley Publishing Asia Pty Ltd.

The influences of canopy species and topographic variables on understory species diversity and composition in coniferous forests.

PubMed

Huo, Hong; Feng, Qi; Su, Yong-hong

2014-01-01

Understanding the factors that influence the distribution of understory vegetation is important for biological conservation and forest management. We compared understory species composition by multi-response permutation procedure and indicator species analysis between plots dominated by Qinghai spruce (Picea crassifolia Kom.) and Qilian juniper (Sabina przewalskii Kom.) in coniferous forests of the Qilian Mountains, northwestern China. Understory species composition differed markedly between the forest types. Many heliophilous species were significantly associated with juniper forest, while only one species was indicative of spruce forest. Using constrained ordination and the variation partitioning model, we quantitatively assessed the relative effects of two sets of explanatory variables on understory species composition. The results showed that topographic variables had higher explanatory power than did site conditions for understory plant distributions. However, a large amount of the variation in understory species composition remained unexplained. Forward selection revealed that understory species distributions were primarily affected by elevation and aspect. Juniper forest had higher species richness and α-diversity and lower β-diversity in the herb layer of the understory plant community than spruce forest, suggesting that the former may be more important in maintaining understory biodiversity and community stability in alpine coniferous forest ecosystems.

Human land use promotes the abundance and diversity of exotic species on caribbean islands.

PubMed

Jesse, Wendy A M; Behm, Jocelyn E; Helmus, Matthew R; Ellers, Jacintha

2018-05-31

Human land use causes major changes in species abundance and composition, yet native and exotic species can exhibit different responses to land use change. Native populations generally decline in human-impacted habitats while exotic species often benefit. In this study, we assessed the effects of human land use on exotic and native reptile diversity, including functional diversity, which relates to the range of habitat use strategies in biotic communities. We surveyed 114 reptile communities from localities that varied in habitat structure and human impact level on two Caribbean islands, and calculated species richness, overall abundance and evenness for every plot. Functional diversity indices were calculated using published trait data, which enabled us to detect signs of trait filtering associated with impacted habitats. Our results show that environmental variation among sampling plots was explained by two PCA ordination axes related to habitat structure (i.e. forest or non-forest) and human impact level (i.e. addition of man-made constructions such as roads and buildings). Several diversity indices were significantly correlated with the two PCA axes, but exotic and native species showed opposing responses. Native species reached the highest abundance in forests, while exotic species were absent in this habitat. Human impact was associated with an increase in exotic abundance and species richness, while native species showed no significant associations. Functional diversity was highest in non-forested environments on both islands, and further increased on St. Martin with the establishment of functionally unique exotic species in non-forested habitat. Habitat structure, rather than human impact, proved to be an important agent for environmental filtering of traits, causing divergent functional trait values across forested and non-forested environments. Our results illustrate the importance of considering various elements of land use when studying its impact on

Parametric scaling from species to growth-form diversity: an interesting analogy with multifractal functions.

PubMed

Ricotta, Carlo; Pacini, Alessandra; Avena, Giancarlo

2002-01-01

We propose a measure of divergence from species to life-form diversity aimed at summarizing the ecological similarity among different plant communities without losing information on traditional taxonomic diversity. First, species and life-form relative abundances within a given plant community are determined. Next, using Rényi's generalized entropy, the diversity profiles of the analyzed community are computed both from species and life-form relative abundances. Finally, the speed of decrease from species to life-form diversity is obtained by combining the outcome of both profiles. Interestingly, the proposed measure shows some formal analogies with multifractal functions developed in statistical physics for the analysis of spatial patterns. As an application for demonstration, a small data set from a plant community sampled in the archaeological site of Paestum (southern Italy) is used.

Limits to randomness in paleobiologic models: the case of Phanerozoic species diversity

NASA Technical Reports Server (NTRS)

Sepkoski, J. J. Jr; Sepkoski JJ, J. r. (Principal Investigator)

1994-01-01

The question of how random, or unconstrained, paleobiologic models should be is examined with a case study: Signor's (1982, 1985) inverse calculation of levels of marine species diversity through the Phanerozoic. His calculation involved an ingenious model that estimated species numbers and species abundances in the world oceans of the past by correcting known numbers of fossil species for variations in sedimentary rocks available for sampling and in effort paleontologists might devote to sampling. The model proves robust to changes in possible shapes of species-abundance distributions, but it is sensitive to alterations in the assumption that paleontologists collect fossils at random. If it is assumed that ease of collecting varies with age of sediment (with the Cenozoic offering easy sampling) or that paleontologists tend to seek out rarer fossils, results of the inverse calculation change. In particular, the magnitude of the calculated Cenozoic diversity increase always declines from the factor of about seven as originally reported to something considerably smaller. This leaves open the problem of the magnitude of Cenozoic increase in marine species diversity, awaiting better empirical data and, perhaps, more exacting models, random or otherwise.

Consumer species richness and nutrients interact in determining producer diversity

PubMed Central

Groendahl, Sophie; Fink, Patrick

2017-01-01

While it is crucial to understand the factors that determine the biodiversity of primary producer communities, the relative importance of bottom-up and top-down control factors is still poorly understood. Using freshwater benthic algal communities in the laboratory as a model system, we find an unimodal relationship between nutrient availability and producer diversity, and that increasing number of consumer species increases producer diversity, but overall grazing decreases algal biodiversity. Interestingly, these two factors interact strongly in determining producer diversity, as an increase in nutrient supply diminishes the positive effect of consumer species richness on producer biodiversity. This novel and thus-far overlooked interaction of bottom-up and top-down control mechanisms of biodiversity may have a pronounced impact on ecosystem functioning and thus have repercussions for the fields of biodiversity conservation and restoration. PMID:28303953

Assessment of plant species diversity based on hyperspectral indices at a fine scale.

PubMed

Peng, Yu; Fan, Min; Song, Jingyi; Cui, Tiantian; Li, Rui

2018-03-19

Fast and nondestructive approaches of measuring plant species diversity have been a subject of excessive scientific curiosity and disquiet to environmentalists and field ecologists worldwide. In this study, we measured the hyperspectral reflectances and plant species diversity indices at a fine scale (0.8 meter) in central Hunshandak Sandland of Inner Mongolia, China. The first-order derivative value (FD) at each waveband and 37 hyperspectral indices were used to assess plant species diversity. Results demonstrated that the stepwise linear regression of FD can accurately estimate the Simpson (R 2  = 0.83), Pielou (R 2  = 0.87) and Shannon-Wiener index (R 2  = 0.88). Stepwise linear regression of FD (R 2  = 0.81, R 2  = 0.82) and spectral vegetation indices (R 2  = 0.51, R 2  = 0.58) significantly predicted the Margalef and Gleason index. It was proposed that the Simpson, Pielou and Shannon-Wiener indices, which are widely used as plant species diversity indicators, can be precisely estimated through hyperspectral indices at a fine scale. This research promotes the development of methods for assessment of plant diversity using hyperspectral data.

Measures of School Integration: Comparing Coleman's Index to Measures of Species Diversity.

ERIC Educational Resources Information Center

Mercil, Steven Bray; Williams, John Delane

This study used species diversity indices developed in ecology as a measure of socioethnic diversity, and compared them to Coleman's Index of Segregation. The twelve indices were Simpson's Concentration Index ("ell"), Simpson's Index of Diversity, Hurlbert's Probability of Interspecific Encounter (PIE), Simpson's Probability of…

Pediatric Helicobacter pylori gastropathy demonstrates a unique pattern of gastric foveolar hyperplasia.

PubMed

Saghier, Sadaf; Schwarz, Steven M; Anderson, Virginia; Gupta, Raavi; Heidarian, Amin; Rabinowitz, Simon S

2018-04-25

Helicobacter pylori (Hp) are the most common agents causing gastric mucosal injury worldwide. Foveolar hyperplasia is a key component of the stomach's reaction to injury. This study examines histopathologic characteristics associated with Helicobacter pylori and with non- Helicobacter pylori-associated gastropathy in children and adolescents, and compares the prevalence of foveolar hyperplasia among these disease subgroups and normal control subjects. Eighty-one gastric antral and corpus biopsies from subjects 2-19 years of age were studied. Twenty-two subjects with Helicobacter pylori gastritis were compared to 23 with non-Helicobacter pylori gastropathy and to 36 controls (normal biopsies). Foveolar length, full mucosal thickness, and the foveolar length: full mucosal thickness ratio were derived by a morphometric technique previously developed to analyze adult gastric tissue. Compared to controls, Helicobacter pylori gastritis demonstrated significant increases in antral foveolar length (P < .0001), full mucosal thickness (P < .0001), as well as corpus foveolar length (P < .05) and corpus full mucosal thickness (P < .05). Non-Helicobacter pylori-associated gastropathy also was characterized by increased antral foveolar length (P < .0001) and full mucosal thickness (P < .001) but corresponding corpus measurements did not differ from controls. Antral foveolar length in non-Helicobacter pylori gastropathy was increased, when compared to Helicobacter pylori gastritis (P < .05), while corpus values were not. The non-Helicobacter pylori gastropathy group demonstrated increased antral foveolar length: full mucosal thickness ratios, compared with Helicobacter pylori gastritis (P < .001) and with normal controls (P < .0001). An objective, quantitative approach to measuring foveolar hyperplasia in adults was successfully applied to pediatric biopsies and yielded a richer characterization of gastric pathology in children. Foveolar hyperplasia appears to

Under-estimation of genetic diversity within wild potato (Solanum) species populations

USDA-ARS?s Scientific Manuscript database

Genebanks seek to know the partitioning of diversity among species, populations, and individuals in the collection, since this informs decisions for adopting the most effective approaches to collecting, maintaining and evaluating that diversity. Recent reports suggest that heterogeneity within gene...

Evolution of sociality in spiders leads to depleted genomic diversity at both population and species levels.

PubMed

Settepani, V; Schou, M F; Greve, M; Grinsted, L; Bechsgaard, J; Bilde, T

2017-08-01

Across several animal taxa, the evolution of sociality involves a suite of characteristics, a "social syndrome," that includes cooperative breeding, reproductive skew, primary female-biased sex ratio, and the transition from outcrossing to inbreeding mating system, factors that are expected to reduce effective population size (Ne). This social syndrome may be favoured by short-term benefits but come with long-term costs, because the reduction in Ne amplifies loss of genetic diversity by genetic drift, ultimately restricting the potential of populations to respond to environmental change. To investigate the consequences of this social life form on genetic diversity, we used a comparative RAD-sequencing approach to estimate genomewide diversity in spider species that differ in level of sociality, reproductive skew and mating system. We analysed multiple populations of three independent sister-species pairs of social inbreeding and subsocial outcrossing Stegodyphus spiders, and a subsocial outgroup. Heterozygosity and within-population diversity were sixfold to 10-fold lower in social compared to subsocial species, and demographic modelling revealed a tenfold reduction in Ne of social populations. Species-wide genetic diversity depends on population divergence and the viability of genetic lineages. Population genomic patterns were consistent with high lineage turnover, which homogenizes the genetic structure that builds up between inbreeding populations, ultimately depleting genetic diversity at the species level. Indeed, species-wide genetic diversity of social species was 5-8 times lower than that of subsocial species. The repeated evolution of species with this social syndrome is associated with severe loss of genomewide diversity, likely to limit their evolutionary potential. © 2017 John Wiley & Sons Ltd.

Operational Tree Species Mapping in a Diverse Tropical Forest with Airborne Imaging Spectroscopy

PubMed Central

Baldeck, Claire A.; Asner, Gregory P.; Martin, Robin E.; Anderson, Christopher B.; Knapp, David E.; Kellner, James R.; Wright, S. Joseph

2015-01-01

Remote identification and mapping of canopy tree species can contribute valuable information towards our understanding of ecosystem biodiversity and function over large spatial scales. However, the extreme challenges posed by highly diverse, closed-canopy tropical forests have prevented automated remote species mapping of non-flowering tree crowns in these ecosystems. We set out to identify individuals of three focal canopy tree species amongst a diverse background of tree and liana species on Barro Colorado Island, Panama, using airborne imaging spectroscopy data. First, we compared two leading single-class classification methods—binary support vector machine (SVM) and biased SVM—for their performance in identifying pixels of a single focal species. From this comparison we determined that biased SVM was more precise and created a multi-species classification model by combining the three biased SVM models. This model was applied to the imagery to identify pixels belonging to the three focal species and the prediction results were then processed to create a map of focal species crown objects. Crown-level cross-validation of the training data indicated that the multi-species classification model had pixel-level producer’s accuracies of 94–97% for the three focal species, and field validation of the predicted crown objects indicated that these had user’s accuracies of 94–100%. Our results demonstrate the ability of high spatial and spectral resolution remote sensing to accurately detect non-flowering crowns of focal species within a diverse tropical forest. We attribute the success of our model to recent classification and mapping techniques adapted to species detection in diverse closed-canopy forests, which can pave the way for remote species mapping in a wider variety of ecosystems. PMID:26153693

Helicobacter infections with rare bacteria or minimal gastritis: Expecting the unexpected.

PubMed

Glickman, Jonathan N; Noffsinger, Amy; Nevin, Daniel T; Ray, Mukunda; Lash, Richard H; Genta, Robert M

2015-07-01

The routine use of special stains for detection of Helicobacter remains controversial. To determine the frequency of histologically atypical Helicobacter infection. All gastric biopsies received at a large pathology reference laboratory over a 6-month period were stained for Helicobacter, and the histologic and clinicopathologic parameters evaluated. Amongst 7663 Helicobacter-positive biopsies, 823 (10.7%) did not show typical chronic active gastritis with numerous Helicobacter organisms, and were therefore considered histologically atypical. Rare Helicobacter pylori organisms accounted for 58.0% of all atypical infections; the next most common atypical Helicobacter infection was that with minimal or no gastric inflammation (23.3% of atypical infections). Patients in these groups did not differ demographically from those with other forms of atypical or typical Helicobacter infection, although a small subgroup (6%) was more likely to have had a previously treated infection. In many of these atypical infections, Helicobacter would not have been suspected based on the histologic findings alone, and would have been missed without routine special stains. Performing a sensitive stain could prevent additional testing and allow prompt treatment of the affected patients, thus substantially reducing the risk for peptic ulcer and gastric cancer and preventing the transmission of the infection to family members. Copyright © 2015 Editrice Gastroenterologica Italiana S.r.l. Published by Elsevier Ltd. All rights reserved.

Genetic Diversity in the Paramecium aurelia Species Complex

PubMed Central

Catania, Francesco; Wurmser, François; Potekhin, Alexey A.; Przyboś, Ewa; Lynch, Michael

2009-01-01

Current understanding of the population genetics of free-living unicellular eukaryotes is limited, and the amount of genetic variability in these organisms is still a matter of debate. We characterized—reproductively and genetically—worldwide samples of multiple Paramecium species belonging to a cryptic species complex, Paramecium aurelia, whose species have been shown to be reproductively isolated. We found that levels of genetic diversity both in the nucleus and in the mitochondrion are substantial within groups of reproductively compatible P. aurelia strains but drop considerably when strains are partitioned according to their phylogenetic groupings. Our study reveals the existence of discrepancies between the mating behavior of a number of P. aurelia strains and their multilocus genetic profile, a controversial finding that has major consequences for both the current methods of species assignment and the species problem in the P. aurelia complex. PMID:19023087

A six-year grazing exclusion changed plant species diversity of a Stipa breviflora desert steppe community, northern China.

PubMed

Wang, Xing; Yang, Xinguo; Wang, Lei; Chen, Lin; Song, Naiping; Gu, Junlong; Xue, Yi

2018-01-01

Excluding grazers is one of most efficient ways to restore degraded grasslands in desert-steppe communities, but may negatively affect the recovery of plant species diversity. However, diversity differences between grazed and fenced grasslands in desert-steppe are poorly known. In a Stipa breviflora desert steppe community in Northern China, we established six plots to examine spatial patterns of plant species diversity under grazed and fenced conditions, respectively. We addressed three aspects of species diversity: (1) The logistic, exponential and power models were used to describe the species-area curve (SAR). Species richness, abundance and Shannon diversity values change differently with increasing sampling areas inside and outside of the fence. The best fitted model for SAR was the logistic model. Excluding grazers had a significant impact on the shape of SAR. (2) Variograms was applied to examine the spatial characteristics of plant species diversity. We found strong spatial autocorrelations in the diversity variables both inside and outside the fence. After grazing exclusion, the spatial heterogeneity decreased in species richness, increased in abundance and did not change in Shannon diversity. (3) We used variance partitioning to determine the relative contributions of spatial and environmental factors to plant species diversity patterns. Environmental factors explained the largest proportion of variation in species diversity, while spatial factors contributed little. Our results suggest that grazing enclosures decreased species diversity patterns and the spatial pattern of the S. breviflora desert steppe community was predictable.

A six-year grazing exclusion changed plant species diversity of a Stipa breviflora desert steppe community, northern China

PubMed Central

Wang, Xing; Yang, Xinguo; Wang, Lei; Chen, Lin; Gu, Junlong; Xue, Yi

2018-01-01

Excluding grazers is one of most efficient ways to restore degraded grasslands in desert-steppe communities, but may negatively affect the recovery of plant species diversity. However, diversity differences between grazed and fenced grasslands in desert-steppe are poorly known. In a Stipa breviflora desert steppe community in Northern China, we established six plots to examine spatial patterns of plant species diversity under grazed and fenced conditions, respectively. We addressed three aspects of species diversity: (1) The logistic, exponential and power models were used to describe the species-area curve (SAR). Species richness, abundance and Shannon diversity values change differently with increasing sampling areas inside and outside of the fence. The best fitted model for SAR was the logistic model. Excluding grazers had a significant impact on the shape of SAR. (2) Variograms was applied to examine the spatial characteristics of plant species diversity. We found strong spatial autocorrelations in the diversity variables both inside and outside the fence. After grazing exclusion, the spatial heterogeneity decreased in species richness, increased in abundance and did not change in Shannon diversity. (3) We used variance partitioning to determine the relative contributions of spatial and environmental factors to plant species diversity patterns. Environmental factors explained the largest proportion of variation in species diversity, while spatial factors contributed little. Our results suggest that grazing enclosures decreased species diversity patterns and the spatial pattern of the S. breviflora desert steppe community was predictable. PMID:29456890

Comparative nucleotide diversity across North American and European populus species.

PubMed

Ismail, Mohamed; Soolanayakanahally, Raju Y; Ingvarsson, Pär K; Guy, Robert D; Jansson, Stefan; Silim, Salim N; El-Kassaby, Yousry A

2012-06-01

Nucleotide polymorphisms in two North American balsam poplars (Populus trichocarpa Torr. & Gray and P. balsamifera L.; section Tacamahaca), and one Eurasian aspen (P. tremula L.; section Populus) were compared using nine loci involved in defense, stress response, photoperiodism, freezing tolerance, and housekeeping. Nucleotide diversity varied among species and was highest for P. tremula (θ(w) = 0.005, π(T) = 0.007) as compared to P. balsamifera (θ(w) = 0.004, π(T) = 0.005) or P. trichocarpa (θ(w) = 0.002, π(T) = 0.003). Across species, the defense and the stress response loci accounted for the majority of the observed level of nucleotide diversity. In general, the studied loci did not deviate from neutral expectation either at the individual locus (non-significant normalized Fay and Wu's H) or at the multi-locus level (non-significant HKA test). Using molecular clock analysis, section Tacamahaca probably shared a common ancestor with section Populus approximately 4.5 million year ago. Divergence between the two closely related balsam poplars was about 0.8 million years ago, a pattern consistent with an isolation-with-migration (IM) model. As expected, P. tremula showed a five-fold higher substitution rate (2 × 10(-8) substitution/site/year) compared to the North American species (0.4 × 10(-8) substitution/site/year), probably reflecting its complex demographic history. Linkage disequilibrium (LD) varied among species with a more rapid decay in the North American species (<400 bp) in comparison to P. tremula (≫400 bp). The similarities in nucleotide diversity pattern and LD decay of the two balsam poplar species likely reflects the recent time of their divergence.

Diverse effects of degree of urbanisation and forest size on species richness and functional diversity of plants, and ground surface-active ants and spiders.

PubMed

Melliger, Ramona Laila; Braschler, Brigitte; Rusterholz, Hans-Peter; Baur, Bruno

2018-01-01

Urbanisation is increasing worldwide and is regarded a major driver of environmental change altering local species assemblages in urban green areas. Forests are one of the most frequent habitat types in urban landscapes harbouring many native species and providing important ecosystem services. By using a multi-taxa approach covering a range of trophic ranks, we examined the influence of degree of urbanisation and forest size on the species richness and functional diversity of plants, and ground surface-active ants and spiders. We conducted field surveys in twenty-six forests in the urban region of Basel, Switzerland. We found that a species' response to urbanisation varied depending on trophic rank, habitat specificity and the diversity indices used. In plants, species richness decreased with degree of urbanisation, whereas that of both arthropod groups was not affected. However, ants and spiders at higher trophic rank showed greater shifts in species composition with increasing degree of urbanisation, and the percentage of forest specialists in both arthropod groups increased with forest size. Local abiotic site characteristics were also crucial for plant species diversity and species composition, while the structural diversity of both leaf litter and vegetation was important for the diversity of ants and spiders. Our results highlight that even small urban forests can harbour a considerable biodiversity including habitat specialists. Nonetheless, urbanisation directly and indirectly caused major shifts in species composition. Therefore, special consideration needs to be given to vulnerable species, including those with special habitat requirements. Locally adapted management practices could be a step forward to enhance habitat quality in a way to maximize diversity of forest species and thus ensure forest ecosystem functioning; albeit large-scale factors also remain important.

Modern and Interglacial Marine Ostracode Species Diversity Patterns off Eastern North America

NASA Astrophysics Data System (ADS)

Chiu, W. T. R.; Yasuhara, M.; Cronin, T. M.; Hunt, G.; Gemery, L.

2016-02-01

Latitudinal species diversity gradients (LSDGs) are a major feature of various marine groups. However, the detailed shape of LSDG in each marine taxonomic group and the causes of the diversity patterns, notably climatic factors, are still controversial due to limited sampling of many taxa in the world's oceans. We analyzed benthic podocopid ostracode faunal assemblages on the continental shelf regions from Arctic to tropical regions off eastern North America to determine biodiversity patterns and their relationships to oceanographic conditions (temperature, productivity, etc). Our database consists of 200 ostracode species from more than 100 bottom sediment samples. Preliminary results suggest that biodiversity, as measured using simple diversity (S), rarefaction, Shannon and α-Fisher indices, show strong latitudinal diversity gradients in which diversity is 2 to 3 times higher in tropical and subtropical regions that in northern high latitude areas. These modern ostracode diversity patterns will be compared with those from past interglacial periods of global warmth during the Pliocene and Pleistocene to assess the impact of warmer-than- present climate conditions on diversity.

Cloning of Helicobacter suis cholesterol α-glucosyltransferase and production of an antibody capable of detecting it in formalin-fixed, paraffin-embedded gastric tissue sections.

PubMed

Kawakubo, Masatomo; Horiuchi, Kazuki; Komura, Hitomi; Sato, Yoshiko; Kato, Masayoshi; Ikeyama, Meguru; Fukushima, Mana; Yamada, Shigenori; Ishizone, Satoshi; Matsumoto, Takehisa; Ota, Hiroyoshi; Sagara, Junji; Nakayama, Jun

2017-10-01

Helicobacter suis (H. suis), formerly called Helicobacter heilmannii type 1 (H. heilmannii), is a gram-negative bacterium of the Helicobacter species. This pathogen infects the stomach of humans and animals such as dogs, cats, pigs, and rodents, the latter giving rise to zoonotic infection. Here, we generated a H. suis-specific antibody useful for immunohistochemistry with formalin-fixed, paraffin-embedded tissue sections. To do so, we began by cloning the gene encoding H. suis cholesterol α-glucosyltransferase (αCgT). αCgT is the key enzyme responsible for biosynthesis of cholesteryl α-D-glucopyranoside (CGL), a major cell wall component of Helicobacter species including H. suis. The deduced amino acid sequence of H. suis αCgT had 56% identity with the corresponding Helicobacter pylori (H. pylori). We then developed a polyclonal antibody (anti-Hh-I205R) by immunizing rabbits with a 205 amino acid H. suis αCgT fragment. Immunohistochemistry with the anti-Hh-I205R antibody could differentiate H. suis from H. pylori in gastric mucosa sections derived from mice infected with either pathogen. We then probed formalin-fixed, paraffin-embedded sections of human gastric mucosa positive for H. suis infection with the anti-Hh-I205R antibody and detected positive staining. These results indicate that anti-Hh-I205R antibody is specific for H. suis αCgT and useful to detect H. suis in gastric specimens routinely analyzed in pathological examinations.

Multiscale mapping of species diversity under changed land use using imaging spectroscopy.

PubMed

Paz-Kagan, Tarin; Caras, Tamir; Herrmann, Ittai; Shachak, Moshe; Karnieli, Arnon

2017-07-01

Land use changes are one of the most important factors causing environmental transformations and species diversity alterations. The aim of the current study was to develop a geoinformatics-based framework to quantify alpha and beta diversity indices in two sites in Israel with different land uses, i.e., an agricultural system of fruit orchards, an afforestation system of planted groves, and an unmanaged system of groves. The framework comprises four scaling steps: (1) classification of a tree species distribution (SD) map using imaging spectroscopy (IS) at a pixel size of 1 m; (2) estimation of local species richness by calculating the alpha diversity index for 30-m grid cells; (3) calculation of beta diversity for different land use categories and sub-categories at different sizes; and (4) calculation of the beta diversity difference between the two sites. The SD was classified based on a hyperspectral image with 448 bands within the 380-2500 nm spectral range and a spatial resolution of 1 m. Twenty-three tree species were classified with high overall accuracy values of 82.57% and 86.93% for the two sites. Significantly high values of the alpha index characterize the unmanaged land use, and the lowest values were calculated for the agricultural land use. In addition, high values of alpha indices were found at the borders between the polygons related to the "edge-effect" phenomenon, whereas low alpha indices were found in areas with high invasion species rates. The beta index value, calculated for 58 polygons, was significantly lower in the agricultural land use. The suggested framework of this study succeeded in quantifying land use effects on tree species distribution, evenness, and richness. IS and spatial statistics techniques offer an opportunity to study woody plant species variation with a multiscale approach that is useful for managing land use, especially under increasing environmental changes. © 2017 by the Ecological Society of America.

Interactive effects between plant functional types and soil factors on tundra species diversity and community composition.

PubMed

Iturrate-Garcia, Maitane; O'Brien, Michael J; Khitun, Olga; Abiven, Samuel; Niklaus, Pascal A; Schaepman-Strub, Gabriela

2016-11-01

Plant communities are coupled with abiotic factors, as species diversity and community composition both respond to and influence climate and soil characteristics. Interactions between vegetation and abiotic factors depend on plant functional types (PFT) as different growth forms will have differential responses to and effects on site characteristics. However, despite the importance of different PFT for community assembly and ecosystem functioning, research has mainly focused on vascular plants. Here, we established a set of observational plots in two contrasting habitats in northeastern Siberia in order to assess the relationship between species diversity and community composition with soil variables, as well as the relationship between vegetation cover and species diversity for two PFT (nonvascular and vascular). We found that nonvascular species diversity decreased with soil acidity and moisture and, to a lesser extent, with soil temperature and active layer thickness. In contrast, no such correlation was found for vascular species diversity. Differences in community composition were found mainly along soil acidity and moisture gradients. However, the proportion of variation in composition explained by the measured soil variables was much lower for nonvascular than for vascular species when considering the PFT separately. We also found different relationships between vegetation cover and species diversity according the PFT and habitat. In support of niche differentiation theory, species diversity and community composition were related to edaphic factors. The distinct relationships found for nonvascular and vascular species suggest the importance of considering multiple PFT when assessing species diversity and composition and their interaction with edaphic factors. Synthesis : Identifying vegetation responses to edaphic factors is a first step toward a better understanding of vegetation-soil feedbacks under climate change. Our results suggest that incorporating

Molecular analyses reveal high species diversity of trematodes in a sub-Arctic lake

USGS Publications Warehouse

Soldánová, Miroslava; Georgieva, Simona; Roháčováa, Jana; Knudsen, Rune; Kuhn, Jesper A.; Henriksen, Eirik H.; Siwertsson, Anna; Shaw, Jenny C.; Kuris, Armand M.; Amundsen, Per-Arne; Scholz, Tomáš; Lafferty, Kevin D.; Kostadinova, Aneta

2017-01-01

To identify trematode diversity and life-cycles in the sub-Arctic Lake Takvatn, Norway, we characterised 120 trematode isolates from mollusc first intermediate hosts, metacercariae from second intermediate host fishes and invertebrates, and adults from fish and invertebrate definitive hosts, using molecular techniques. Phylogenies based on nuclear and/or mtDNA revealed high species richness (24 species or species-level genetic lineages), and uncovered trematode diversity (16 putative new species) from five families typical in lake ecosystems (Allocreadiidae, Diplostomidae, Plagiorchiidae, Schistosomatidae and Strigeidae). Sampling potential invertebrate hosts allowed matching of sequence data for different stages, thus achieving molecular elucidation of trematode life-cycles and exploration of host-parasite interactions. Phylogenetic analyses also helped identify three major mollusc intermediate hosts (Radix balthica, Pisidium casertanum and Sphaerium sp.) in the lake. Our findings increase the known trematode diversity at the sub-Arctic Lake Takvatn, showing that digenean diversity is high in this otherwise depauperate sub-Arctic freshwater ecosystem, and indicating that sub-Arctic and Arctic ecosystems may be characterised by unique trematode assemblages.

Genetic diversity of calcareous grassland plant species depends on historical landscape configuration.

PubMed

Reisch, Christoph; Schmidkonz, Sonja; Meier, Katrin; Schöpplein, Quirin; Meyer, Carina; Hums, Christian; Putz, Christina; Schmid, Christoph

2017-04-24

Habitat fragmentation is considered to be a main reason for decreasing genetic diversity of plant species. However, the results of many fragmentation studies are inconsistent. This may be due to the influence of habitat conditions, having an indirect effect on genetic variation via reproduction. Consequently we took a comparative approach to analyse the impact of habitat fragmentation and habitat conditions on the genetic diversity of calcareous grassland species in this study. We selected five typical grassland species (Primula veris, Dianthus carthusianorum, Medicago falcata, Polygala comosa and Salvia pratensis) occurring in 18 fragments of calcareous grasslands in south eastern Germany. We sampled 1286 individuals in 87 populations and analysed genetic diversity using amplified fragment length polymorphisms. Additionally, we collected data concerning habitat fragmentation (historical and present landscape structure) and habitat conditions (vegetation structure, soil conditions) of the selected study sites. The whole data set was analysed using Bayesian multiple regressions. Our investigation indicated a habitat loss of nearly 80% and increasing isolation between grasslands since 1830. Bayesian analysis revealed a significant impact of the historical landscape structure, whereas habitat conditions played no important role for the present-day genetic variation of the studied plant species. Our study indicates that the historical landscape structure may be more important for genetic diversity than present habitat conditions. Populations persisting in abandoned grassland fragments may contribute significantly to the species' variability even under deteriorating habitat conditions. Therefore, these populations should be included in approaches to preserve the genetic variation of calcareous grassland species.

Transcriptome Complexity and Riboregulation in the Human Pathogen Helicobacter pylori

PubMed Central

Pernitzsch, Sandy R.; Sharma, Cynthia M.

2012-01-01

The Gram-negative Epsilonproteobacterium Helicobacter pylori is considered as one of the major human pathogens and many studies have focused on its virulence mechanisms as well as genomic diversity. In contrast, only very little is known about post-transcriptional regulation and small regulatory RNAs (sRNAs) in this spiral-shaped microaerophilic bacterium. Considering the absence of the common RNA chaperone Hfq, which is a key-player in post-transcriptional regulation in enterobacteria, H. pylori was even regarded as an organism without riboregulation. However, analysis of the H. pylori primary transcriptome using RNA-seq revealed a very complex transcriptional output from its small genome. Furthermore, the identification of a wealth of sRNAs as well as massive antisense transcription indicates that H. pylori uses riboregulation for its gene expression control. The ongoing functional characterization of sRNAs along with the identification of associated RNA binding proteins will help to understand their potential roles in Helicobacter virulence and stress response. Moreover, research on riboregulation in H. pylori will provide new insights into its virulence mechanisms and will also help to shed light on post-transcriptional regulation in other Epsilonproteobacteria, including widespread and emerging pathogens such as Campylobacter. PMID:22919606

Morphological and Phytochemical Diversity among Hypericum Species of the Mediterranean Basin

PubMed Central

Nürk, Nicolai M.; Crockett, Sara L.

2012-01-01

The genus Hypericum L. (St. John’s wort, Hypericaceae) includes more than 450 species that occur in temperature or tropical mountain regions of the world. Monographic work on the genus has resulted in the recognition and description of 36 taxonomic sections, delineated by specific combinations of morphological characteristics and biogeographic distribution. The Mediterranean Basin has been recognized as a hot spot of diversity for the genus Hypericum, and as such is a region in which many endemic species occur. Species belonging to sections distributed in this area of the world display considerable morphological and phytochemical diversity. Results of a cladistic analysis, based on 89 morphological characters that were considered phylogenetically informative, are given here. In addition, a brief overview of morphological characteristics and the distribution of pharmaceutically relevant secondary metabolites for species native to this region of the world are presented. PMID:22662020

Detection of Helicobacter spp. DNA in the oral cavity of dogs.

PubMed

Recordati, Camilla; Gualdi, Valentina; Tosi, Sabrina; Facchini, Roberto Vailati; Pengo, Graziano; Luini, Mario; Simpson, Kenneth W; Scanziani, Eugenio

2007-01-31

The mode of acquisition of gastric Helicobacter spp. infection in dogs has not been determined. It is suspected that oral-oral and faecal-oral transmission may be involved. The present study sought to determine if Helicobacter spp. DNA is present in the oral cavity of healthy and vomiting dogs. Thirty-eight pet dogs (27 vomiting and 11 clinically healthy) were studied. The presence of Helicobacter spp. was determined by single and nested PCR evaluation of DNA extracted from saliva, dental plaque and gastric biopsy samples. Helicobacter spp. DNA was detected by nested PCR in 36 (94.7%) gastric biopsies, 17 (44.7%) dental plaque and 19 (50%) saliva samples out of the 38 dogs examined. Overall 27 (71.1%) dogs screened by nested PCR were found to harbour Helicobacter spp. DNA in the oral cavity (dental plaque and/or saliva). There was no significant difference in the prevalence of Helicobacter spp. DNA in the oral cavity of vomiting and healthy dogs, and the time from vomiting to oral sampling did not have significant impact. This study confirms the high prevalence of gastric Helicobacter spp. infection in dogs, and reveals that Helicobacter spp. DNA is detectable in the oral cavity of over 70% of dogs. These findings support the possibility of oral-oral transmission between dogs and that the canine oral cavity may act as source of non-pylori Helicobacter spp. infection for humans.

Medicinal plants in the treatment of Helicobacter pylori infections.

PubMed

Safavi, Maliheh; Shams-Ardakani, Mohammadreza; Foroumadi, Alireza

2015-07-01

Helicobacter pylori is a small, spiral, Gram-negative bacillus that plays a role in the pathogenesis of a number of diseases ranging from asymptomatic gastritis to gastric cancer. Schedule compliance, antibiotic drug resistance, and side-effects of triple or quadruple therapy have led to research for novel candidates from plants. The purpose of this paper is to review the most potent medicinal plants of recently published literature with anti-H. pylori activity. For centuries, herbals have been used by traditional healers around the world to treat various gastrointestinal tract disorders such as dyspepsia, gastritis, and peptic ulcer disease. The mechanism of action by which these botanicals exert their therapeutic properties has not been completely and clearly elucidated. Anti-H. pylori properties may be one of the possible mechanisms by which gastroprotective herbs treat gastrointestinal tract disorders. Electronic databases such as PubMed, Google scholar, EBSCO, and local databases were explored for medicinal plants with anti-H. pylori properties between 1984 and 2013 using key words "medicinal plants" and "Helicobacter pylori" or "anti-Helicobacter pylori". A total of 43 medicinal plant species belonging to 27 families including Amaryllidaceae, Anacardiaceae, Apiaceae, Apocynaceae, Asclepiadoideae, Asteraceae, Bignoniaceae, Clusiaceae, Chancapiedra, Combretaceae, Cyperaceae, Euphorbiaceae, Fabaceae, Geraniaceae, Lamiaceae, Lauraceae, Lythraceae, Menispermaceae, Myristicaceae, Myrtaceae, Oleaceae, Papaveraceae, Plumbaginaceae, Poaceae, Ranunculaceae, Rosaceae, and Theaceae were studied as herbs with potent anti-H. pylori effects. Traditional folk medicinal use of some of these plants to treat gastric infections is substantiated by the antibacterial activity of their extracts against H. pylori.

Unexpected Variation in Neuroanatomy among Diverse Nematode Species

PubMed Central

Han, Ziduan; Boas, Stephanie; Schroeder, Nathan E.

2016-01-01

Nematodes are considered excellent models for understanding fundamental aspects of neuron function. However, nematodes are less frequently used as models for examining the evolution of nervous systems. While the habitats and behaviors of nematodes are diverse, the neuroanatomy of nematodes is often considered highly conserved. A small number of nematode species greatly influences our understanding of nematode neurobiology. The free-living species Caenorhabditis elegans and, to a lesser extent, the mammalian gastrointestinal parasite Ascaris suum are, historically, the primary sources of knowledge regarding nematode neurobiology. Despite differences in size and habitat, C. elegans and A. suum share a surprisingly similar neuroanatomy. Here, we examined species across several clades in the phylum Nematoda and show that there is a surprising degree of neuroanatomical variation both within and among nematode clades when compared to C. elegans and Ascaris. We found variation in the numbers of neurons in the ventral nerve cord and dye-filling pattern of sensory neurons. For example, we found that Pristionchus pacificus, a bacterial feeding species used for comparative developmental research had 20% fewer ventral cord neurons compared to C. elegans. Steinernema carpocapsae, an insect-parasitic nematode capable of jumping behavior, had 40% more ventral cord neurons than C. elegans. Interestingly, the non-jumping congeneric nematode, S. glaseri showed an identical number of ventral cord neurons as S. carpocapsae. There was also variability in the timing of neurodevelopment of the ventral cord with two of five species that hatch as second-stage juveniles showing delayed neurodevelopment. We also found unexpected variation in the dye-filling of sensory neurons among examined species. Again, sensory neuron dye-filling pattern did not strictly correlate with phylogeny. Our results demonstrate that variation in nematode neuroanatomy is more prevalent than previously assumed and

The Phytophthora species assemblage and diversity in riparian alder ecosystems of western Oregon, USA.

PubMed

Sims, Laura Lee; Sutton, Wendy; Reeser, Paul; Hansen, Everett M

2015-01-01

Phytophthora species were systematically sampled, isolated, identified and compared for presence in streams, soil and roots of alder (Alnus species) dominated riparian ecosystems in western Oregon. We describe the species assemblage and evaluate Phytophthora diversity associated with alder. We recovered 1250 isolates of 20 Phytophthora species. Only three species were recovered from all substrates (streams, soil, alder roots): P. gonapodyides, the informally described "P. taxon Pgchlamydo", and P. siskiyouensis. P. alni ssp. uniformis along with five other species not previously recovered in Oregon forests are included in the assemblage: P.citricola s.l., P. gregata, P. gallica, P. nicotianae and P. parsiana. Phytophthora species diversity was greatest in downstream riparian locations. There was no significant difference in species diversity comparing soil and unwashed roots (the rhizosphere) to stream water. There was a difference between the predominating species from the rhizosphere compared to stream water. The most numerous species was the informally described "P. taxon Oaksoil", which was mainly recovered from, and most predominant in, stream water. The most common species from riparian forest soils and alder root systems was P. gonapodyides. © 2015 by The Mycological Society of America.

Effect of host diversity and species assemblage composition on bovine tuberculosis (bTB) risk in Ethiopian cattle.

PubMed

Sintayehu, Dejene W; Heitkönig, Ignas M A; Prins, Herbert H T; Tessema, Zewdu K; DE Boer, Willem F

2017-05-01

Current theories on diversity-disease relationships describe host species diversity and species identity as important factors influencing disease risk, either diluting or amplifying disease prevalence in a community. Whereas the simple term 'diversity' embodies a set of animal community characteristics, it is not clear how different measures of species diversity are correlated with disease risk. We therefore tested the effects of species richness, Pielou's evenness and Shannon's diversity on bovine tuberculosis (bTB) risk in cattle in the Afar Region and Awash National Park between November 2013 and April 2015. We also analysed the identity effect of a particular species and the effect of host habitat use overlap on bTB risk. We used the comparative intradermal tuberculin test to assess the number of bTB-infected cattle. Our results suggested a dilution effect through species evenness. We found that the identity effect of greater kudu - a maintenance host - confounded the dilution effect of species diversity on bTB risk. bTB infection was positively correlated with habitat use overlap between greater kudu and cattle. Different diversity indices have to be considered together for assessing diversity-disease relationships, for understanding the underlying causal mechanisms. We posit that unpacking diversity metrics is also relevant for formulating disease control strategies to manage cattle in ecosystems characterized by seasonally limited resources and intense wildlife-livestock interactions.

No evidence for Helicobacter pylori in oral lichen planus.

PubMed

Hulimavu, Shwetha R; Mohanty, Leeky; Tondikulam, Narayan V; Shenoy, Sadhana; Jamadar, Saleha; Bhadranna, Abhishek

2014-09-01

Oral lichen planus is a T-cell-mediated mucosal disease of unknown etiology. Numerous predisposing factors have been put forward in the etiology of this disease. This includes stress, drugs, genetic susceptibility, certain viruses, and bacterial infections. Recently, there have been studies published on possible role of Helicobacter pylori infection in pathogenesis of mucocutaneous diseases including oral lichen planus (OLP). The aim of this study was to detect immunohistochemically the presence of Helicobacter pylori in oral lichen planus. Paraffin-embedded tissue blocks of 50 cases of OLP and 10 cases of normal buccal mucosal biopsies and 6 endoscopic biopsies of patients with peptic ulcer (control group) were sectioned and stained by hematoxylin and eosin. Serial sections of same were stained immunohistochemically using Anti-Helicobacter pylori antibody and observed under microscope for presence or absence of Helicobacter pylori. Except for the control group, none of the cases of OLP and normal buccal mucosal biopsies showed positivity for Helicobacter pylori. As we did not detect the presence of Helicobacter pylori in any of the OLP cases, we question the role of these organisms in the pathogenesis of OLP planus if any. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

The Prevalence of Mixed Helicobacter pylori Infections in Symptomatic and Asymptomatic Subjects in Dhaka, Bangladesh.

PubMed

Kibria, Khandoker Mohammad K; Hossain, Md Enayet; Sultana, Jinath; Sarker, Shafiqul A; Bardhan, Pradip Kumar; Rahman, Motiur; Nahar, Shamsun

2015-10-01

Helicobacter pylori is a highly genetically diverse bacterial species, which can persist in the gastric environment for decades. Recent studies have shown that single infections predominate in developed countries, whereas mixed infections are more prevalent in developing countries. Mixed infections of this bacterium may be important for adaptation to the hostile gastric environment and may facilitate dyspeptic symptoms. To calculate the prevalence of mixed infections in symptomatic and asymptomatic subjects, 2010 H. pylori isolates collected from 83 symptomatic and 91 asymptomatic subjects from Dhaka, Bangladesh, were analyzed by (i) random amplified polymorphic DNA fingerprinting (RAPD) and (ii) multiplex PCR amplification for cagA and vacA virulence gene alleles. The overall prevalence of mixed H. pylori infection was 60.15% (77/128), indicating substantial co-colonization in this population. We additionally found that symptomatic subjects (53%) had a significantly higher rate of mixed infection than asymptomatic individuals (36.3%) (p = .016) and that the prevalence of the cagA and vacA and vacA m1/s1 and vacA m2/s1 alleles were higher in subjects with mixed infection. Our findings suggest that an increased diversity of the H. pylori strains in the gastric environment may contribute to the development of disease symptoms. © 2015 John Wiley & Sons Ltd.

An approach to bioassessment of water quality using diversity measures based on species accumulative curves.

PubMed

Xu, Guangjian; Zhang, Wei; Xu, Henglong

2015-02-15

Traditional community-based bioassessment is time-consuming because they rely on full species-abundance data of a community. To improve bioassessment efficiency, the feasibility of the diversity measures based on species accumulative curves for bioassessment of water quality status was studied based on a dataset of microperiphyton fauna. The results showed that: (1) the species accumulative curves well fitted the Michaelis-Menten equation; (2) the β- and γ-diversity, as well as the number of samples to 50% of the maximum species number (Michaelis-Menten constant K), can be statistically estimated based on the formulation; (3) the rarefied α-diversity represented a significant negative correlation with the changes in the nutrient NH4-N; and (4) the estimated β-diversity and the K constant were significantly positively related to the concentration of NH4-N. The results suggest that the diversity measures based on species accumulative curves might be used as a potential bioindicator of water quality in marine ecosystems. Copyright © 2014 Elsevier Ltd. All rights reserved.

Functional diversity supports the physiological tolerance hypothesis for plant species richness along climatic gradients

USGS Publications Warehouse

Spasojevic, Marko J.; Grace, James B.; Harrison, Susan; Damschen, Ellen Ingman

2013-01-01

1. The physiological tolerance hypothesis proposes that plant species richness is highest in warm and/or wet climates because a wider range of functional strategies can persist under such conditions. Functional diversity metrics, combined with statistical modeling, offer new ways to test whether diversity-environment relationships are consistent with this hypothesis. 2. In a classic study by R. H. Whittaker (1960), herb species richness declined from mesic (cool, moist, northerly) slopes to xeric (hot, dry, southerly) slopes. Building on this dataset, we measured four plant functional traits (plant height, specific leaf area, leaf water content and foliar C:N) and used them to calculate three functional diversity metrics (functional richness, evenness, and dispersion). We then used a structural equation model to ask if ‘functional diversity’ (modeled as the joint responses of richness, evenness, and dispersion) could explain the observed relationship of topographic climate gradients to species richness. We then repeated our model examining the functional diversity of each of the four traits individually. 3. Consistent with the physiological tolerance hypothesis, we found that functional diversity was higher in more favorable climatic conditions (mesic slopes), and that multivariate functional diversity mediated the relationship of the topographic climate gradient to plant species richness. We found similar patterns for models focusing on individual trait functional diversity of leaf water content and foliar C:N. 4. Synthesis. Our results provide trait-based support for the physiological tolerance hypothesis, suggesting that benign climates support more species because they allow for a wider range of functional strategies.

Crop Species Diversity Changes in the United States: 1978–2012

PubMed Central

Aguilar, Jonathan; Gramig, Greta G.; Hendrickson, John R.; Archer, David W.; Forcella, Frank; Liebig, Mark A.

2015-01-01

Anecdotal accounts regarding reduced US cropping system diversity have raised concerns about negative impacts of increasingly homogeneous cropping systems. However, formal analyses to document such changes are lacking. Using US Agriculture Census data, which are collected every five years, we quantified crop species diversity from 1978 to 2012, for the contiguous US on a county level basis. We used Shannon diversity indices expressed as effective number of crop species (ENCS) to quantify crop diversity. We then evaluated changes in county-level crop diversity both nationally and for each of the eight Farm Resource Regions developed by the National Agriculture Statistics Service. During the 34 years we considered in our analyses, both national and regional ENCS changed. Nationally, crop diversity was lower in 2012 than in 1978. However, our analyses also revealed interesting trends between and within different Resource Regions. Overall, the Heartland Resource Region had the lowest crop diversity whereas the Fruitful Rim and Northern Crescent had the highest. In contrast to the other Resource Regions, the Mississippi Portal had significantly higher crop diversity in 2012 than in 1978. Also, within regions there were differences between counties in crop diversity. Spatial autocorrelation revealed clustering of low and high ENCS and this trend became stronger over time. These results show that, nationally counties have been clustering into areas of either low diversity or high diversity. Moreover, a significant trend of more counties shifting to lower rather than to higher crop diversity was detected. The clustering and shifting demonstrates a trend toward crop diversity loss and attendant homogenization of agricultural production systems, which could have far-reaching consequences for provision of ecosystem system services associated with agricultural systems as well as food system sustainability. PMID:26308552

Multivariate analysis of morphological diversity among closely related Daucus species and subspecies in Tunisia

USDA-ARS?s Scientific Manuscript database

The genus Daucus includes about 20-25 species worldwide. Northern Africa represents a major center of diversity of Daucus, with Tunisia thought to contain 11 species and seven subspecies. We assessed morphological diversity from a Daucus germplasm collection of 103 accessions at the National Gene Ba...

Diverse effects of degree of urbanisation and forest size on species richness and functional diversity of plants, and ground surface-active ants and spiders

PubMed Central

Melliger, Ramona Laila; Rusterholz, Hans-Peter; Baur, Bruno

2018-01-01

Urbanisation is increasing worldwide and is regarded a major driver of environmental change altering local species assemblages in urban green areas. Forests are one of the most frequent habitat types in urban landscapes harbouring many native species and providing important ecosystem services. By using a multi-taxa approach covering a range of trophic ranks, we examined the influence of degree of urbanisation and forest size on the species richness and functional diversity of plants, and ground surface-active ants and spiders. We conducted field surveys in twenty-six forests in the urban region of Basel, Switzerland. We found that a species’ response to urbanisation varied depending on trophic rank, habitat specificity and the diversity indices used. In plants, species richness decreased with degree of urbanisation, whereas that of both arthropod groups was not affected. However, ants and spiders at higher trophic rank showed greater shifts in species composition with increasing degree of urbanisation, and the percentage of forest specialists in both arthropod groups increased with forest size. Local abiotic site characteristics were also crucial for plant species diversity and species composition, while the structural diversity of both leaf litter and vegetation was important for the diversity of ants and spiders. Our results highlight that even small urban forests can harbour a considerable biodiversity including habitat specialists. Nonetheless, urbanisation directly and indirectly caused major shifts in species composition. Therefore, special consideration needs to be given to vulnerable species, including those with special habitat requirements. Locally adapted management practices could be a step forward to enhance habitat quality in a way to maximize diversity of forest species and thus ensure forest ecosystem functioning; albeit large-scale factors also remain important. PMID:29920553

Individuals and the variation needed for high species diversity in forest trees

Treesearch

James S. Clark

2010-01-01

In the past, explanations for high species diversity have been sought at the species level. Theory shows that coexistence requires substantial differences between species, but species-level data rarely provide evidence for such differences. Using data from forests in the southeastern United States, I show here that variation evident at the individual level provides for...

Prevalence and risk factors of Helicobacter pylori infection in Chinese maritime workers.

PubMed

Hu, Dongmei; Shao, Jing; Wang, Ligang; Zheng, Huichun; Xu, Yan; Song, Guirong; Liu, Qigui

2013-01-01

Helicobacter pylori infection is very common worldwide. To evaluate the prevalence and identify the risk factors for Helicobacter pylori infection in Chinese maritime workers. Between March 2010 and October 2010, 3995 subjects were selected in the Hospital of Dalian Port. The presence of Helicobacter pylori infection was confirmed using laboratory tests (serum IgG anti-Helicobacter pylori antibodies) and background information, family history, lifestyle and eating habits were collected using questionnaires. The prevalence of Helicobacter pylori infection was 44.9% in these Chinese maritime workers. Prevalence of Helicobacter pylori infection was associated with family income, living space, family history of gastrointestinal diseases, smoking, drinking tea, raw vegetables consumption, spicy food, pickle food, dining outside, no regular meal and dish sharing. Further analysis with multivariate logistic regression analysis indicated that raw vegetables consumption, pickle food consumption, family income and family history of gastrointestinal diseases were independent predictors for Helicobacter pylori infection. No association was found between infection and gender, marital status, education, alcohol consumption and tap water consumption. Helicobacter pylori infection is associated with raw vegetables consumption, pickle food consumption, family income and family history of gastrointestinal disease among Chinese maritime workers.

Anti-inflammatory and cytoprotective effects of selected Pakistani medicinal plants in Helicobacter pylori-infected gastric epithelial cells.

PubMed

Zaidi, Syed Faisal; Muhammad, Jibran Sualeh; Shahryar, Saeeda; Usmanghani, Khan; Gilani, Anwarul-Hassan; Jafri, Wasim; Sugiyama, Toshiro

2012-05-07

Helicobacter pylori infection is associated with gastritis, peptic ulcer, and gastric cancer. Due to its high global prevalence and uprising resistance to available antibiotics, efforts are now directed to identify alternative source to treat and prevent associated disorders. In the present study, effect of selected indigenous medicinal plants of Pakistan was evaluated on the secretion of interleukin-8 (IL-8) and generation of reactive oxygen species (ROS) in a bid to rationalize their medicinal use and to examine the anti-inflammatory and cytoprotective effects in gastric epithelial cells. AGS cells and clinically isolated Helicobacter pylori strain (193C) were employed for co-culture experiments. Anti-Helicobacter pylori activity and cytotoxic effects of the selected plants were determined by serial dilution method and DNA fragmentation assay respectively. ELISA and flow cytometry were performed to evaluate the effect on IL-8 secretion and ROS generation in Helicobacter pylori-infected cells. At 100μg/ml, extracts of Alpinia galangal, Cinnamomum cassia, Cinnamomum tamala, Mentha arvensis, Myrtus communis, Oligochaeta ramose, Polygonum bistorta, Rosa damascena, Ruta graveolens, Syzygium aromaticum, Tamarix dioica, and Terminalia chebula exhibited strong inhibitory activity against IL-8 secretion. Of these, four extracts of Cinnamomum cassia, Myrtus communis, Syzygium aromaticum, and Terminalia chebula markedly inhibited IL-8 secretion at both 50 and 100μg/ml. Cinnamomum cassia was further assessed at different concentrations against Helicobacter pylori and TNF-α stimulated IL-8 secretion, which displayed significant suppression of IL-8 in a concentration-dependent-manner. Among the plants examined against ROS generation, Achillea millefolium, Berberis aristata, Coriandrum sativum, Foeniculum vulgare, Matricaria chamomilla and Prunus domestica demonstrated significant suppression of ROS from Helicobacter pylori-infected cells (p<0.01). Results of the study

Identification of and Screening for Human Helicobacter cinaedi Infections and Carriers via Nested PCR

PubMed Central

Oyama, Kohta; Khan, Shahzada; Okamoto, Tatsuya; Fujii, Shigemoto; Ono, Katsuhiko; Matsunaga, Tetsuro; Yoshitake, Jun; Sawa, Tomohiro; Tomida, Junko; Kawamura, Yoshiaki

2012-01-01

Helicobacter cinaedi is the most frequently reported enterohepatic Helicobacter species isolated from humans. Earlier research suggested that certain patients with H. cinaedi infection may remain undiagnosed or incorrectly diagnosed because of difficulties in detecting the bacteria by conventional culture methods. Here, we report a nested PCR assay that rapidly detects the cytolethal distending toxin gene (cdt) of H. cinaedi with high specificity and sensitivity. Specificity of the assay was validated by using different species of Helicobacter and Campylobacter, as well as known H. cinaedi-positive and -negative samples. The sensitivity of detection for the cdt gene in the assay was 102 CFU/ml urine or 102 CFU/105 infected RAW 264.7 cells. In an H. cinaedi-infected mouse model, the cdt gene of H. cinaedi was effectively detected via the assay with urine (6/7), stool (2/3), and blood (2/6) samples. Importantly, it detected H. cinaedi in blood, urine, and stool samples from one patient with a suspected H. cinaedi infection and three patients with known infections. The assay was further used clinically to follow up two H. cinaedi-infected patients after antibiotic treatment. Stool samples from these two patients evaluated by nested PCR after antibiotic therapy showed clearance of bacterial DNA. Finally, analysis of stool specimens from healthy volunteers showed occasional positive reactions (4/30) to H. cinaedi DNA, which suggests intestinal colonization by H. cinaedi in healthy subjects. In conclusion, this nested PCR assay may be useful for the rapid diagnosis, antimicrobial treatment evaluation, and epidemiological study of H. cinaedi infection. PMID:23015666

Helicobacter Pylori Infections

MedlinePlus

Helicobacter pylori (H. pylori) is a type of bacteria that causes infection in the stomach. It is the main cause of ... of people in the United States get an H. pylori infection. Most people get it as a ...

Species diversity and environmental determinants of aquatic and terrestrial communities invaded by Alternanthera philoxeroides.

PubMed

Wu, Hao; Carrillo, Juli; Ding, Jianqing

2017-03-01

The impact of invasive species on native biodiversity varies across environments, with invasion effects of amphibious plant species across terrestrial and aquatic systems especially poorly understood. In this study, we established 29 terrestrial plots and 23 aquatic plots which were invaded by the alien plant alligator weed, Alternanthera philoxeroides in Southern China. We measured α-species diversity (Shannon-Wiener and Simpson index), species richness and evenness, species cover and the importance value (a comprehensive index of cover, height and abundance) of A. philoxeroides in invaded communities in both aquatic and terrestrial habitats. We recorded seven environmental factors (longitude, latitude, elevation above sea level, temperature, precipitation, ammonia and nitrate) across habitats. We then used Redundancy Analysis (RDA) to determine which factors best explain A. philoxeroides invasion in either environment type. We found that terrestrial habitats had greater species diversity (Shannon index) than aquatic habitats, and the biotic resistance of aquatic plant communities to the A. philoxeroides invasion was weaker than terrestrial plant communities. Accumulated ammonia improved some indices of species diversity (Shannon-Weiner, Simpson) and evenness, but decreased species cover of A. philoxeroides in both aquatic and terrestrial environments. Precipitation increased species richness in terrestrial habitats but decreased richness in aquatic habitats. Precipitation increased A. philoxeroides cover in both environment types, while elevated nitrate increased A. philoxeroides cover in terrestrial habitats only. In aquatic habitats, species richness increased but A. philoxeroides cover decreased with increasing longitude. Our study indicates that increased precipitation may accelerate A. philoxeroides spread across aquatic and terrestrial habitats, while reducing nitrate inputs could inhibit terrestrial A. philoxeroides invasion. Aquatic communities appear to

Invasive plants have scale-dependent effects on diversity by altering species-area relationships.

PubMed

Powell, Kristin I; Chase, Jonathan M; Knight, Tiffany M

2013-01-18

Although invasive plant species often reduce diversity, they rarely cause plant extinctions. We surveyed paired invaded and uninvaded plant communities from three biomes. We reconcile the discrepancy in diversity loss from invaders by showing that invaded communities have lower local richness but steeper species accumulation with area than that of uninvaded communities, leading to proportionately fewer species loss at broader spatial scales. We show that invaders drive scale-dependent biodiversity loss through strong neutral sampling effects on the number of individuals in a community. We also show that nonneutral species extirpations are due to a proportionately larger effect of invaders on common species, suggesting that rare species are buffered against extinction. Our study provides a synthetic perspective on the threat of invasions to biodiversity loss across spatial scales.

Microsatellite Analysis of Museum Specimens Reveals Historical Differences in Genetic Diversity between Declining and More Stable Bombus Species.

PubMed

Maebe, Kevin; Meeus, Ivan; Ganne, Maarten; De Meulemeester, Thibaut; Biesmeijer, Koos; Smagghe, Guy

2015-01-01

Worldwide most pollinators, e.g. bumblebees, are undergoing global declines. Loss of genetic diversity can play an essential role in these observed declines. In this paper, we investigated the level of genetic diversity of seven declining Bombus species and four more stable species with the use of microsatellite loci. Hereto we genotyped a unique collection of museum specimens. Specimens were collected between 1918 and 1926, in 6 provinces of the Netherlands which allowed us to make interspecific comparisons of genetic diversity. For the stable species B. pascuorum, we also selected populations from two additional time periods: 1949-1955 and 1975-1990. The genetic diversity and population structure in B. pascuorum remained constant over the three time periods. However, populations of declining bumblebee species showed a significantly lower genetic diversity than co-occurring stable species before their major declines. This historical difference indicates that the repeatedly observed reduced genetic diversity in recent populations of declining bumblebee species is not caused solely by the decline itself. The historically low genetic diversity in the declined species may be due to the fact that these species were already rare, making them more vulnerable to the major drivers of bumblebee decline.

Digenean species diversity in teleost fishes from the Gulf of Gabes, Tunisia (Western Mediterranean)

PubMed Central

Derbel, H.; Châari, M.; Neifar, L.

2012-01-01

This study is the first attempt to survey the diversity of fish digeneans in the Gulf of Gabes (southern coast of Tunisia). A total of 779 fishes belonging to 32 species were sampled. 53 species of Digenea belonging to 15 families were recorded. Among these species, 24 are reported for the first time from the coast of Tunisia. We report one new host record, Lecithochirium sp. from Sardinella aurita. The Hemiuridae is the dominant family. A host-parasite list is presented with the information on the prevalence, abundance and mean intensity of each species collected. The diversity of Digenea is compared with other localities in the Mediterranean Sea and the northern east of Tunisia. The Gulf of Gabes shows the lowest diversity linked to the anthropogenic activities and impact of exotic species. The use of Digenea as indicators of the state of the ecosystem is discussed. PMID:22550623

Virulence Factors of Helicobacter pylori: A Review

PubMed Central

Roesler, Bruna M.; Rabelo-Gonçalves, Elizabeth M.A.; Zeitune, José M.R.

2014-01-01

Helicobacter pylori is a spiral-shaped Gram-negative bacterium that colonizes the human stomach and can establish a long-term infection of the gastric mucosa, a condition that affects the relative risk of developing various clinical disorders of the upper gastrointestinal tract, such as chronic gastritis, peptic ulcer disease, mucosa-associated lymphoid tissue (MALT) lymphoma, and gastric adenocarcinoma. H. pylori presents a high-level of genetic diversity, which can be an important factor in its adaptation to the host stomach and also for the clinical outcome of infection. There are important H. pylori virulence factors that, along with host characteristics and the external environment, have been associated with the different occurrences of diseases. This review is aimed to analyzing and summarizing the main of them and possible associations with the clinical outcome. PMID:24833944

Species richness and traits predict overyielding in stem growth in an early-successional tree diversity experiment.

PubMed

Grossman, Jake J; Cavender-Bares, Jeannine; Hobbie, Sarah E; Reich, Peter B; Montgomery, Rebecca A

2017-10-01

Over the last two decades, empirical work has established that higher biodiversity can lead to greater primary productivity; however, the importance of different aspects of biodiversity in contributing to such relationships is rarely elucidated. We assessed the relative importance of species richness, phylogenetic diversity, functional diversity, and identity of neighbors for stem growth 3 yr after seedling establishment in a tree diversity experiment in eastern Minnesota. Generally, we found that community-weighted means of key functional traits (including mycorrhizal association, leaf nitrogen and calcium, and waterlogging tolerance) as well as species richness were strong, independent predictors of stem biomass growth. More phylogenetically diverse communities did not consistently produce more biomass than expected, and the trait values or diversity of individual functional traits better predicted biomass production than did a multidimensional functional diversity metric. Furthermore, functional traits and species richness best predicted growth at the whole-plot level (12 m 2 ), whereas neighborhood composition best predicted growth at the focal tree level (0.25 m 2 ). The observed effects of biodiversity on growth appear strongly driven by positive complementary effects rather than by species-specific selection effects, suggesting that synergistic species' interactions rather than the influence of a few important species may drive overyielding. © 2017 by the Ecological Society of America.

Patterns of oribatid mite species diversity: testing the effects of elevation, area and sampling effort.

PubMed

Mumladze, Levan; Murvanidze, Maka; Maraun, Mark

2017-07-01

Elevational gradients in species diversity and species area relationships are two well established patterns that are not mutually exclusive in space and time. Elevation and area are both considered as good proxies to detect and characterize the patterns of species diversity distribution. However, such studies are hampered by the incomplete biodiversity data available for ecologists, which may affect the pattern perceptions. Using the large dataset of oribatid mite communities sampled in Georgia, we tested the effects of altitude and area on species distribution using various approaches, while explicitly considering the biases from sampling effort. Our results showed that elevation and area are strongly correlated (with increasing absolute elevation, land area decreases) and both have strong linear effects on species diversity distribution when studied separately. Approaches based on multiple regression and direct removal of co-varied factors, indicated that the effect of area can actually override the effect of elevation in describing the oribatid species diversity distribution along with elevation. On the other hand, the bias of sampling proved significant in perception of elevational species richness pattern with less effect on elevational species area relationship. We suggest that the sampling alone may be responsible for patterns observed and thus should be considered in ecological studies when eligible.

Genetic diversity in three endangered pitcher plant species (Sarracenia; Sarraceniaceae) is lower than widespread congeners.

PubMed

Furches, M Steven; Small, Randall L; Furches, Anna

2013-10-01

Narrow-ranging, rare species often exhibit levels of genetic diversity lower than more common or widespread congeners. These taxa are at increased risk of extinction due to threats associated with natural as well as anthropogenic events. We assessed genetic variation in three federally endangered Sarracenia species. We discuss maintenance of genetic diversity and evolutionary implications of rarity. • We analyzed three noncoding chloroplast regions and nine microsatellite loci in populations spanning the geographic ranges of S. oreophila, S. alabamensis, and S. jonesii. The same microsatellite loci were used to examine a single field site of three more widespread species (S. alata, S. leucophylla, and S. rubra subsp. wherryi). • All three endangered species have experienced reductions in population size and numbers. All show considerably less variation than more widespread members of the genus. Sarracenia alabamensis maintains the greatest microsatellite variation but has the fewest remaining populations and may be under the greatest threat. More widespread S. oreophila maintains surprising chloroplast diversity, yet exhibits little microsatellite diversity. Sarracenia jonesii lacks chloroplast diversity, yet maintains greater microsatellite diversity than S. oreophila. • The three endangered species differ in levels and structure of diversity, yet not in predictable ways, emphasizing that unique demographic and ecological histories, rather than current distribution and population size, best explain present patterns of genetic variation. Maintenance of remaining genetic variation is important, but preventing further habitat loss and degradation is critical.

Comparative analysis of microsatellites in five different antagonistic Trichoderma species for diversity assessment.

PubMed

Rai, Shalini; Kashyap, Prem Lal; Kumar, Sudheer; Srivastava, Alok Kumar; Ramteke, Pramod W

2016-01-01

Microsatellites provide an ideal molecular markers system to screen, characterize and evaluate genetic diversity of several fungal species. Currently, there is very limited information on the genetic diversity of antagonistic Trichoderma species as determined using a range of molecular markers. In this study, expressed and whole genome sequences available in public database were used to investigate the occurrence, relative abundance and relative density of SSRs in five different antagonistic Trichoderma species: Trichoderma atroviride, T. harzianum, T. reesei, T. virens and T. asperellum. Fifteen SSRs loci were used to evaluate genetic diversity of twenty isolates of Trichoderma spp. from different geographical regions of India. Results indicated that relative abundance and relative density of SSRs were higher in T. asperellum followed by T. reesei and T. atroviride. Tri-nucleotide repeats (80.2%) were invariably the most abundant in all species. The abundance and relative density of SSRs were not influenced by the genome sizes and GC content. Out of eighteen primer sets, only 15 primer pairs showed successful amplification in all the test species. A total of 24 alleles were detected and five loci were highly informative with polymorphism information content values greater than 0.40, these markers provide useful information on genetic diversity and population genetic structure, which, in turn, can exploit for establishing conservation strategy for antagonistic Trichoderma isolates.

[Species, functional, structural diversity of typical plant communities and their responses to environmental factors in Miao Archipelago, China.

PubMed

Zheng, Li Ting; Su, Tian; Liu, Xiang Yu; Yin, Fang; Guo, Chao; Tuo, Bin; Yan, En Rong

2018-02-01

Island vegetation plays an important role in biodiversity research across the world. The study of plant diversity in island is helpful for understanding the mechanism of plant diversity maintenance under land-sea interaction. Here, four typical plant communities (Quercus acutissima community, Robinia pseudoacacia community, Pinus thunbergii community and Vitex negundo community) in Miao Archipelago were selected to examine the species, functional and structural diversities and their responses to environmental factors at the community scale by using species diversity indices, functional diversity indices, as well as structural diversity indices. The results showed that the species richness and Rao index of P. thunbergii community was higher than that of Q. acutissima community and R. pseudoacacia community, but the structural diversity was lower. The species diversity and structural diversity of V. Negundo shrub were lower than that of forest community, but the functional diversity was higher than some forest communities. The relationship between the diversity of typical plant communities in island area illustrated a significant positive correlation between species richness with Rao index and tree height diversity, however the correlation with functional evenness was significantly negative. The structural diversity and functional evenness were determined by slope with negative and positive relationships, respectively. Functional heterogeneity, functional divergence and species diversity were affected largely by soil physical and chemical properties, displaying the positive relationship with soil bulk density and soil total carbon content, and a negative relationship with soil water content. In conclusion, diversity pattern of plant community in Miao Archipelago reflected not only the characteristics in mainland vegetation but also the special nature of the sea island.

Soil fauna and leaf species, but not species diversity, affect initial soil erosion in a subtropical forest plantation

NASA Astrophysics Data System (ADS)

Seitz, Steffen; Goebes, Philipp; Assmann, Thorsten; Schuldt, Andreas; Scholten, Thomas

2017-04-01

In subtropical parts of China, high rainfall intensities cause continuous soil losses and thereby provoke severe harms to ecosystems. In woodlands, it is not the tree canopy, but mostly an intact forest floor that provides protection from soil erosion. Although the protective role of leaf litter covers against soil losses is known for a long time, little research has been conducted on the processes involved. For instance, the role of different leaf species and leaf species diversity has been widely disregarded. Furthermore, the impact of soil meso- and macrofauna within the litter layer on soil losses remains unclear. To investigate how leaf litter species and diversity as well as soil meso- and macrofauna affect sediment discharge in a subtropical forest ecosystem, a field experiment was carried out in Xingangshan, Jiangxi Province, PR China (BEF China). A full-factorial random design with 96 micro-scale runoff plots and seven domestic leaf species in three diversity levels and a bare ground feature were established. Erosion was initiated with a rainfall simulator. This study confirms that leaf litter cover generally protects forest soils from water erosion (-82 % sediment discharge on leaf covered plots compared to bare plots) and this protection is gradually removed as the litter layer decomposes. Different leaf species showed variable impacts on sediment discharge and thus erosion control. This effect can be related to different leaf habitus, leaf decomposition rates and food preferences of litter decomposing meso- and macrofauna. In our experiment, runoff plots with leaf litter from Machilus thunbergii in monoculture showed the highest sediment discharge (68.0 g m-2), whereas plots with Cyclobalanopsis glauca in monoculture showed the smallest rates (7.9 g m-2). At the same time, neither leaf species diversity, nor functional diversity showed any significant influence, only a negative trend could be observed. Nevertheless, the protective effect of the leaf

Stabilizing effects in temporal fluctuations: management, traits, and species richness in high-diversity communities.

PubMed

Lepš, Jan; Májeková, Maria; Vítová, Alena; Doležal, Jiří; de Bello, Francesco

2018-02-01

The loss of biodiversity is thought to have adverse effects on multiple ecosystem functions, including the decline of community stability. Decreased diversity reduces the strength of the portfolio effect, a mechanism stabilizing community temporal fluctuations. Community stability is also expected to decrease with greater variability in individual species populations and with synchrony of their fluctuations. In semi-natural meadows, eutrophication is one of the most important drivers of diversity decline; it is expected to increase species fluctuations and synchrony among them, all effects leading to lower community stability. With a 16-year time series of biomass data from a temperate species-rich meadow with fertilization and removal of the dominant species, we assessed population biomass temporal (co)variation under different management types and competition intensity, and in relation to species functional traits and to species diversity. Whereas the effect of dominant removal was relatively small (with a tendency toward lower stability), fertilization markedly decreased community stability (i.e., increased coefficient of variation in the total biomass) and species diversity. On average, the fluctuations of individual populations were mutually independent, with a slight tendency toward synchrony in unfertilized plots, and a tendency toward compensatory dynamics in fertilized plots and no effects of removal. The marked decrease of synchrony with fertilization, contrary to the majority of the results reported previously, follows the predictions of increased compensatory dynamics with increased asymmetric competition for light in a more productive environment. Synchrony increased also with species functional similarity stressing the importance of shared ecological strategies in driving similar species responses to weather fluctuations. As expected, the decrease of temporal stability of total biomass was mainly related to the decrease of species richness, with its

Supporting local diversity of habitats and species on farmland: a comparison of three wildlife-friendly schemes.

PubMed

Hardman, Chloe J; Harrison, Dominic P G; Shaw, Pete J; Nevard, Tim D; Hughes, Brin; Potts, Simon G; Norris, Ken

2016-02-01

Restoration and maintenance of habitat diversity have been suggested as conservation priorities in farmed landscapes, but how this should be achieved and at what scale are unclear. This study makes a novel comparison of the effectiveness of three wildlife-friendly farming schemes for supporting local habitat diversity and species richness on 12 farms in England.The schemes were: (i) Conservation Grade (Conservation Grade: a prescriptive, non-organic, biodiversity-focused scheme), (ii) organic agriculture and (iii) a baseline of Entry Level Stewardship (Entry Level Stewardship: a flexible widespread government scheme). Conservation Grade farms supported a quarter higher habitat diversity at the 100-m radius scale compared to Entry Level Stewardship farms. Conservation Grade and organic farms both supported a fifth higher habitat diversity at the 250-m radius scale compared to Entry Level Stewardship farms. Habitat diversity at the 100-m and 250-m scales significantly predicted species richness of butterflies and plants. Habitat diversity at the 100-m scale also significantly predicted species richness of birds in winter and solitary bees. There were no significant relationships between habitat diversity and species richness for bumblebees or birds in summer.Butterfly species richness was significantly higher on organic farms (50% higher) and marginally higher on Conservation Grade farms (20% higher), compared with farms in Entry Level Stewardship. Organic farms supported significantly more plant species than Entry Level Stewardship farms (70% higher) but Conservation Grade farms did not (10% higher). There were no significant differences between the three schemes for species richness of bumblebees, solitary bees or birds. Policy implications . The wildlife-friendly farming schemes which included compulsory changes in management, Conservation Grade and organic, were more effective at increasing local habitat diversity and species richness compared with the less

Regional diversity reverses the negative impacts of an alien predator on local species-poor communities.

PubMed

Loewen, Charlie J G; Vinebrooke, Rolf D

2016-10-01

Species diversity is often an implicit source of biological insurance for communities against the impacts of novel perturbations, such as the introduction of an invasive species. High environmental heterogeneity (e.g., a mountainous gradient) is expected to beget greater regional species diversity and variation in functional traits related to environmental tolerances. Thus, heterogeneous metacommunities are expected to provide more tolerant colonists that buffer stressed local communities in the absence of dispersal limitation. We tested the hypothesis that importation of a regional zooplankton pool assembled from a diverse array of lakes and ponds lessens the impacts of a novel predator on local species-poor alpine communities by increasing response diversity (i.e., diversity of tolerances to environmental change) as mediated by variation in functional traits related to predator evasion. We also tested whether impacts varied with temperature, as warming may modify (e.g., dampen or amplify) invasion effects. An eight-week factorial experiment ([fishless vs. introduced Oncorhynchus mykiss (rainbow trout)] × [ambient temperature vs. heated] × [local vs. local + regional species pool]) was conducted using 32 1,000-L mesocosms. Associations between experimental treatments and species functional traits were tested by R-mode linked to Q-mode (RLQ) and fourth-corner analyses. Although the introduced predator suppressed local species richness and community biomass, colonization by several montane zooplankters reversed these negative effects, resulting in increased species diversity and production. Invasion resistance was unaffected by higher temperatures, which failed to elicit any significance impacts on the community. We discovered that the smaller body sizes of imported species drove functional overcompensation (i.e., increased production) in invaded communities. The observed ecological surprise showed how regionally sourced biodiversity from a highly

Multilocus phylogeny and coalescent species delimitation in Kotschy's gecko, Mediodactylus kotschyi: Hidden diversity and cryptic species.

PubMed

Kotsakiozi, Panayiota; Jablonski, Daniel; Ilgaz, Çetin; Kumlutaş, Yusuf; Avcı, Aziz; Meiri, Shai; Itescu, Yuval; Kukushkin, Oleg; Gvoždík, Václav; Scillitani, Giovanni; Roussos, Stephanos A; Jandzik, David; Kasapidis, Panagiotis; Lymberakis, Petros; Poulakakis, Nikos

2018-08-01

Kotschy's Gecko, Mediodactylus kotschyi, is a small gecko native to southeastern Europe and the Levant. It displays great morphological variation with a large number of morphologically recognized subspecies. However, it has been suggested that it constitutes a species complex of several yet unrecognized species. In this study, we used multilocus sequence data (three mitochondrial and three nuclear gene fragments) to estimate the phylogenetic relationships of 174 specimens from 129 sampling localities, covering a substantial part of the distribution range of the species. Our results revealed high genetic diversity of M. kotschyi populations and contributed to our knowledge about the phylogenetic relationships and the estimation of the divergence times between them. Diversification within M. kotschyi began approximately 15 million years ago (Mya) in the Middle Miocene, whereas the diversification within most of the major clades have been occurred in the last 5 Mya. Species delimitation analysis suggests there exists five species within the complex, and we propose to tentatively recognize the following taxa as full species: M. kotschyi (mainland Balkans, most of Aegean islands, and Italy), M. orientalis (Levant, Cyprus, southern Anatolia, and south-eastern Aegean islands), M. danilewskii (Black Sea region and south-western Anatolia), M. bartoni (Crete), and M. oertzeni (southern Dodecanese Islands). This newly recognized diversity underlines the complex biogeographical history of the Eastern Mediterranean region. Copyright © 2018 Elsevier Inc. All rights reserved.

Species Diversity and Distributional Pattern of Cockroaches in Lahore, Pakistan

PubMed Central

Memona, Hafsa; Manzoor, Farkhanda; Riaz, Saffora

2017-01-01

Background: Cockroaches are found as the most common urban pests of tropical countries, prompting economic and serious health risk problem for humans by carrying microbes and allergens, acting as vector for various pathogens of diseases. The present study was conducted from April 2013 to March 2014 in various human dwelling localities of urban area of district Lahore, Pakistan. Methods: Cockroaches were collected randomly by hand, food baited and sticky traps throughout the year. Four species of cockroaches (Periplaneta Americana (P. amercana), Blattella germanica (B. germanica), Blatta orientalis (B. orientalis), and Blatta lateralis (B. lateralis) were collected and identified from the study site. Results: B. germanica was the most dominant indoor species with highest diversity indices in study areas. Overall cockroach species diversity was highest in July–September, 2013 with highest Simpson index of diversity and Shannon index as well. P. americana was found second broadly distributed in the study area followed by B. orientalis and B. lateralis were intermediately distributed in residential areas and narrowly distributed in hospitals. Residential areas and hospitals were highly infested with B. germanica followed by P. americana. Population index of B. germanica for hospitals was double than residential areas. B. lateralis was observed as displacing B. orientalis in outdoor habitat through competing with its habitat and food sources. Conclusion: The infestation rate of different species depends on availability of food sources, sanitary conditions and climatic conditions. Cockroach infestation can be controlled with knowledge about their biology and behavior, attention to sanitation and effective use of commercial insecticides. PMID:29062850

The beta-diversity of species interactions: Untangling the drivers of geographic variation in plant-pollinator diversity and function across scales.

PubMed

Burkle, Laura A; Myers, Jonathan A; Belote, R Travis

2016-01-01

Geographic patterns of biodiversity have long inspired interest in processes that shape the assembly, diversity, and dynamics of communities at different spatial scales. To study mechanisms of community assembly, ecologists often compare spatial variation in community composition (beta-diversity) across environmental and spatial gradients. These same patterns inspired evolutionary biologists to investigate how micro- and macro-evolutionary processes create gradients in biodiversity. Central to these perspectives are species interactions, which contribute to community assembly and geographic variation in evolutionary processes. However, studies of beta-diversity have predominantly focused on single trophic levels, resulting in gaps in our understanding of variation in species-interaction networks (interaction beta-diversity), especially at scales most relevant to evolutionary studies of geographic variation. We outline two challenges and their consequences in scaling-up studies of interaction beta-diversity from local to biogeographic scales using plant-pollinator interactions as a model system in ecology, evolution, and conservation. First, we highlight how variation in regional species pools may contribute to variation in interaction beta-diversity among biogeographic regions with dissimilar evolutionary history. Second, we highlight how pollinator behavior (host-switching) links ecological networks to geographic patterns of plant-pollinator interactions and evolutionary processes. Third, we outline key unanswered questions regarding the role of geographic variation in plant-pollinator interactions for conservation and ecosystem services (pollination) in changing environments. We conclude that the largest advances in the burgeoning field of interaction beta-diversity will come from studies that integrate frameworks in ecology, evolution, and conservation to understand the causes and consequences of interaction beta-diversity across scales. © 2016 Botanical

Helicobacter cinaedi Induced Typhlocolitis in Rag-2-Deficient Mice

PubMed Central

Shen, Zeli; Feng, Yan; Rickman, Barry; Fox, James G.

2015-01-01

Background Helicobacter cinaedi, an enterohepatic helicobacter species (EHS), is an important human pathogen and is associated with a wide range of diseases, especially in immunocompromised patients. It has been convincingly demonstrated that innate immune response to certain pathogenic enteric bacteria is sufficient to initiate colitis and colon carcinogenesis in recombinase-activating gene (Rag)-2-deficient mice model. To better understand the mechanisms of human IBD and its association with development of colon cancer, we investigated whether H. cinaedi could induce pathological changes noted with murine enterohepatic helicobacter infections in the Rag2−/− mouse model. Materials and Methods Sixty 129SvEv Rag2−/− mice mouse were experimentally or sham infected orally with H. cinaedi strain CCUG 18818. Gastrointestinal pathology and immune responses in infected and control mice were analyzed at 3, 6 and 9 months postinfection (MPI). H. cinaedi colonized the cecum, colon, and stomach in infected mice. Results H. cinaedi induced typhlocolitis in Rag2−/− mice by 3 MPI and intestinal lesions became more severe by 9 MPI. H. cinaedi was also associated with the elevation of proinflammatory cytokines, interferon-γ, tumor-necrosis factor-α, IL-1β, IL-10; iNOS mRNA levels were also upregulated in the cecum of infected mice. However, changes in IL-4, IL-6, Cox-2, and c-myc mRNA expressions were not detected. Conclusions Our results indicated that the Rag2−/− mouse model will be useful to continue investigating the pathogenicity of H. cinaedi, and to study the association of host immune responses in IBD caused by EHS. PMID:25381744

Climate warming promotes species diversity, but with greater taxonomic redundancy, in complex environments

PubMed Central

Thakur, Madhav P.; Tilman, David; Purschke, Oliver; Ciobanu, Marcel; Cowles, Jane; Isbell, Forest; Wragg, Peter D.; Eisenhauer, Nico

2017-01-01

Climate warming is predicted to alter species interactions, which could potentially lead to extinction events. However, there is an ongoing debate whether the effects of warming on biodiversity may be moderated by biodiversity itself. We tested warming effects on soil nematodes, one of the most diverse and abundant metazoans in terrestrial ecosystems, along a gradient of environmental complexity created by a gradient of plant species richness. Warming increased nematode species diversity in complex (16-species mixtures) plant communities (by ~36%) but decreased it in simple (monocultures) plant communities (by ~39%) compared to ambient temperature. Further, warming led to higher levels of taxonomic relatedness in nematode communities across all levels of plant species richness. Our results highlight both the need for maintaining species-rich plant communities to help offset detrimental warming effects and the inability of species-rich plant communities to maintain nematode taxonomic distinctness when warming occur. PMID:28740868

Demosponge diversity from North Sulawesi, with the description of six new species

PubMed Central

Calcinai, Barbara; Bastari, Azzurra; Bavestrello, Giorgio; Bertolino, Marco; Horcajadas, Santiago Bueno; Pansini, Maurizio; Makapedua, Daisy M.; Cerrano, Carlo

2017-01-01

Abstract Sponges are key components of the benthic assemblages and play an important functional role in many ecosystems, especially in coral reefs. The Indonesian coral reefs, located within the so-called “coral triangle”, are among the richest in the world. However, the knowledge of the diversity of sponges and several other marine taxa is far from being complete in the area. In spite of this great biodiversity, most of the information on Indonesian sponges is scattered in old and fragmented literature and comprehensive data about their diversity are still lacking. In this paper, we report the presence of 94 species recorded during different research campaigns mainly from the Marine Park of Bunaken, North Sulawesi. Six species are new for science and seven represent new records for the area. Several others are very poorly known species, sometimes recorded for the second time after their description. For most species, besides field data and detailed descriptions, pictures in vivo are included. Moreover, two new symbiotic sponge associations are described. This work aims to increase the basic knowledge of Indonesian sponge diversity as a prerequisite for monitoring and conservation of this valuable taxon. PMID:28769718

Ecosystem engineering effects on species diversity across ecosystems: a meta-analysis.

PubMed

Romero, Gustavo Q; Gonçalves-Souza, Thiago; Vieira, Camila; Koricheva, Julia

2015-08-01

Ecosystem engineering is increasingly recognized as a relevant ecological driver of diversity and community composition. Although engineering impacts on the biota can vary from negative to positive, and from trivial to enormous, patterns and causes of variation in the magnitude of engineering effects across ecosystems and engineer types remain largely unknown. To elucidate the above patterns, we conducted a meta-analysis of 122 studies which explored effects of animal ecosystem engineers on species richness of other organisms in the community. The analysis revealed that the overall effect of ecosystem engineers on diversity is positive and corresponds to a 25% increase in species richness, indicating that ecosystem engineering is a facilitative process globally. Engineering effects were stronger in the tropics than at higher latitudes, likely because new or modified habitats provided by engineers in the tropics may help minimize competition and predation pressures on resident species. Within aquatic environments, engineering impacts were stronger in marine ecosystems (rocky shores) than in streams. In terrestrial ecosystems, engineers displayed stronger positive effects in arid environments (e.g. deserts). Ecosystem engineers that create new habitats or microhabitats had stronger effects than those that modify habitats or cause bioturbation. Invertebrate engineers and those with lower engineering persistence (<1 year) affected species richness more than vertebrate engineers which persisted for >1 year. Invertebrate species richness was particularly responsive to engineering impacts. This study is the first attempt to build an integrative framework of engineering effects on species diversity; it highlights the importance of considering latitude, habitat, engineering functional group, taxon and persistence of their effects in future theoretical and empirical studies. © 2014 The Authors. Biological Reviews © 2014 Cambridge Philosophical Society.

Interaction of legionella pneumophila and helicobacter pylori with bacterial species isolated from drinking water biofilms

PubMed Central

2011-01-01

Background It is well established that Legionella pneumophila is a waterborne pathogen; by contrast, the mode of Helicobacter pylori transmission remains unknown but water seems to play an important role. This work aims to study the influence of five microorganisms isolated from drinking water biofilms on the survival and integration of both of these pathogens into biofilms. Results Firstly, both pathogens were studied for auto- and co-aggregation with the species isolated from drinking water; subsequently the formation of mono and dual-species biofilms by L. pneumophila or H. pylori with the same microorganisms was investigated. Neither auto- nor co-aggregation was observed between the microorganisms tested. For biofilm studies, sessile cells were quantified in terms of total cells by SYTO 9 staining, viable L. pneumophila or H. pylori cells were quantified using 16 S rRNA-specific peptide nucleic acid (PNA) probes and cultivable cells by standard culture techniques. Acidovorax sp. and Sphingomonas sp. appeared to have an antagonistic effect on L. pneumophila cultivability but not on the viability (as assessed by rRNA content using the PNA probe), possibly leading to the formation of viable but noncultivable (VBNC) cells, whereas Mycobacterium chelonae increased the cultivability of this pathogen. The results obtained for H. pylori showed that M. chelonae and Sphingomonas sp. help this pathogen to maintain cultivability for at least 24 hours. Conclusions It appears that M. chelonae may have an important role in the survival of both pathogens in drinking water. This work also suggests that the presence of some microorganisms can decrease the cultivability of L. pneumophila but not the viability which indicates that the presence of autochthonous microorganisms can lead to misleading results when the safety of water is assessed by cultivable methods alone. PMID:21418578

Microsatellite Analysis of Museum Specimens Reveals Historical Differences in Genetic Diversity between Declining and More Stable Bombus Species

PubMed Central

Maebe, Kevin; Meeus, Ivan; Ganne, Maarten; De Meulemeester, Thibaut; Biesmeijer, Koos; Smagghe, Guy

2015-01-01

Worldwide most pollinators, e.g. bumblebees, are undergoing global declines. Loss of genetic diversity can play an essential role in these observed declines. In this paper, we investigated the level of genetic diversity of seven declining Bombus species and four more stable species with the use of microsatellite loci. Hereto we genotyped a unique collection of museum specimens. Specimens were collected between 1918 and 1926, in 6 provinces of the Netherlands which allowed us to make interspecific comparisons of genetic diversity. For the stable species B. pascuorum, we also selected populations from two additional time periods: 1949–1955 and 1975–1990. The genetic diversity and population structure in B. pascuorum remained constant over the three time periods. However, populations of declining bumblebee species showed a significantly lower genetic diversity than co-occurring stable species before their major declines. This historical difference indicates that the repeatedly observed reduced genetic diversity in recent populations of declining bumblebee species is not caused solely by the decline itself. The historically low genetic diversity in the declined species may be due to the fact that these species were already rare, making them more vulnerable to the major drivers of bumblebee decline. PMID:26061732

Functional analysis of the Helicobacter pullorum N-linked protein glycosylation system.

PubMed

Jervis, Adrian J; Wood, Alison G; Cain, Joel A; Butler, Jonathan A; Frost, Helen; Lord, Elizabeth; Langdon, Rebecca; Cordwell, Stuart J; Wren, Brendan W; Linton, Dennis

2018-04-01

N-linked protein glycosylation systems operate in species from all three domains of life. The model bacterial N-linked glycosylation system from Campylobacter jejuni is encoded by pgl genes present at a single chromosomal locus. This gene cluster includes the pglB oligosaccharyltransferase responsible for transfer of glycan from lipid carrier to protein. Although all genomes from species of the Campylobacter genus contain a pgl locus, among the related Helicobacter genus only three evolutionarily related species (H. pullorum, H. canadensis and H. winghamensis) potentially encode N-linked protein glycosylation systems. Helicobacter putative pgl genes are scattered in five chromosomal loci and include two putative oligosaccharyltransferase-encoding pglB genes per genome. We have previously demonstrated the in vitro N-linked glycosylation activity of H. pullorum resulting in transfer of a pentasaccharide to a peptide at asparagine within the sequon (D/E)XNXS/T. In this study, we identified the first H. pullorum N-linked glycoprotein, termed HgpA. Production of histidine-tagged HgpA in the background of insertional knockout mutants of H. pullorum pgl/wbp genes followed by analysis of HgpA glycan structures demonstrated the role of individual gene products in the PglB1-dependent N-linked protein glycosylation pathway. Glycopeptide purification by zwitterionic-hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry identified six glycosites from five H. pullorum proteins, which was consistent with proteins reactive with a polyclonal antiserum generated against glycosylated HgpA. This study demonstrates functioning of a H. pullorum N-linked general protein glycosylation system.

Species diversity vs. morphological disparity in the light of evolutionary developmental biology

PubMed Central

Minelli, Alessandro

2016-01-01

Background Two indicators of a clade’s success are its diversity (number of included species) and its disparity (extent of morphospace occupied by its members). Many large genera show high diversity with low disparity, while others such as Euphorbia and Drosophila are highly diverse but also exhibit high disparity. The largest genera are often characterized by key innovations that often, but not necessarily, coincide with their diagnostic apomorphies. In terms of their contribution to speciation, apomorphies are either permissive (e.g. flightlessness) or generative (e.g. nectariferous spurs). Scope Except for Drosophila, virtually no genus among those with the highest diversity or disparity includes species currently studied as model species in developmental genetics or evolutionary developmental biology (evo-devo). An evo-devo approach is, however, potentially important to understand how diversity and disparity could rapidly increase in the largest genera currently accepted by taxonomists. The most promising directions for future research and a set of key questions to be addressed are presented in this review. Conclusions From an evo-devo perspective, the evolution of clades with high diversity and/or disparity can be addressed from three main perspectives: (1) evolvability, in terms of release from previous constraints and of the presence of genetic or developmental conditions favouring multiple parallel occurrences of a given evolutionary transition and its reversal; (2) phenotypic plasticity as a facilitator of speciation; and (3) modularity, heterochrony and a coupling between the complexity of the life cycle and the evolution of diversity and disparity in a clade. This simple preliminary analysis suggests a set of topics that deserve priority for scrutiny, including the possible role of saltational evolution in the origination of high diversity and/or disparity, the predictability of morphological evolution following release from a former constraint, and

Species diversity vs. morphological disparity in the light of evolutionary developmental biology.

PubMed

Minelli, Alessandro

2016-04-01

Two indicators of a clade's success are its diversity (number of included species) and its disparity (extent of morphospace occupied by its members). Many large genera show high diversity with low disparity, while others such as Euphorbia and Drosophila are highly diverse but also exhibit high disparity. The largest genera are often characterized by key innovations that often, but not necessarily, coincide with their diagnostic apomorphies. In terms of their contribution to speciation, apomorphies are either permissive (e.g. flightlessness) or generative (e.g. nectariferous spurs). Except for Drosophila, virtually no genus among those with the highest diversity or disparity includes species currently studied as model species in developmental genetics or evolutionary developmental biology (evo-devo). An evo-devo approach is, however, potentially important to understand how diversity and disparity could rapidly increase in the largest genera currently accepted by taxonomists. The most promising directions for future research and a set of key questions to be addressed are presented in this review. From an evo-devo perspective, the evolution of clades with high diversity and/or disparity can be addressed from three main perspectives: (1) evolvability, in terms of release from previous constraints and of the presence of genetic or developmental conditions favouring multiple parallel occurrences of a given evolutionary transition and its reversal; (2) phenotypic plasticity as a facilitator of speciation; and (3) modularity, heterochrony and a coupling between the complexity of the life cycle and the evolution of diversity and disparity in a clade. This simple preliminary analysis suggests a set of topics that deserve priority for scrutiny, including the possible role of saltational evolution in the origination of high diversity and/or disparity, the predictability of morphological evolution following release from a former constraint, and the extent and the possible

[Evaluation and selection of species diversity index under grazing disturbance in alpine mea-dow].

PubMed

Niu, Yu Jie; Yang, Si Wei; Wang, Gui Zhen; Liu, Li; Hua, Li Min

2017-06-18

The research selected the plots of six grazing intensities in an alpine meadow in north-eastern Tibet Plateau in four years (2012-2015) and studied the relation between ten species diversity indexes, including two measured indexes (Richness and Abundance) in field and two indexes of each dominance, evenness, richness, integrated indexes, and grazing intensity as well as grazing time aiming at scientific selection of biodiversity index under grazing disturbance. The results indicated that the abundance was a better index than importance value to calculate biodiversity level because it was more sensitive to grazing disturbance. Dominance indexes, including Berger-Parker and Dominance, were not sensitive to grazing intensity and grazing time because they could not clarify the effect of grazing disturbance on dominant species in plant community. Evenness indexes, including Equitability and Evenness, had not relation with grazing intensity, however, the evenness index had a negative correlation with grazing time and it was not influenced by occasional species as well as the variation coefficient of species abundance. Hereby, the evenness index could be chosen for studying evenness change at temporal scale. Richness indexes, including Menhinick and Margalef, had no relation with grazing time, however, the Margalef index had a positive correlation with grazing intensity and the index was not influenced by occasional species. Integrated index, including Shannon and Simpson indexes, had no relation with grazing intensity, however, the Shannon index had a significant positive correlation with species richness and abundance and the index was not influenced by occasional species, and it significantly increased along grazing time. Hereby, Shannon index could be used as an index of studying plant species diversity in long-term. In ten diversity indexes, only the measured indexes in field, including richness and abundance, were signifi-cantly negatively correlated with grazing

Genetic Diversity in Lens Species Revealed by EST and Genomic Simple Sequence Repeat Analysis

PubMed Central

Dikshit, Harsh Kumar; Singh, Akanksha; Singh, Dharmendra; Aski, Muraleedhar Sidaram; Prakash, Prapti; Jain, Neelu; Meena, Suresh; Kumar, Shiv; Sarker, Ashutosh

2015-01-01

Low productivity of pilosae type lentils grown in South Asia is attributed to narrow genetic base of the released cultivars which results in susceptibility to biotic and abiotic stresses. For enhancement of productivity and production, broadening of genetic base is essentially required. The genetic base of released cultivars can be broadened by using diverse types including bold seeded and early maturing lentils from Mediterranean region and related wild species. Genetic diversity in eighty six accessions of three species of genus Lens was assessed based on twelve genomic and thirty one EST-SSR markers. The evaluated set of genotypes included diverse lentil varieties and advanced breeding lines from Indian programme, two early maturing ICARDA lines and five related wild subspecies/species endemic to the Mediterranean region. Genomic SSRs exhibited higher polymorphism in comparison to EST SSRs. GLLC 598 produced 5 alleles with highest gene diversity value of 0.80. Among the studied subspecies/species 43 SSRs detected maximum number of alleles in L. orientalis. Based on Nei’s genetic distance cultivated lentil L. culinaris subsp. culinaris was found to be close to its wild progenitor L. culinaris subsp. orientalis. The Prichard’s structure of 86 genotypes distinguished different subspecies/species. Higher variability was recorded among individuals within population than among populations. PMID:26381889

Diversity and enzyme activity of Penicillium species associated with macroalgae in Jeju Island.

PubMed

Park, Myung Soo; Lee, Seobihn; Oh, Seung-Yoon; Cho, Ga Youn; Lim, Young Woon

2016-10-01

A total of 28 strains of 19 Penicillium species were isolated in a survey of extracellular enzyme-producing fungi from macroalgae along the coast of Jeju Island of Korea. Penicillium species were identified based on morphological and β-tubulin sequence analyses. In addition, the halo-tolerance and enzyme activity of all strains were evaluated. The diversity of Penicillium strains isolated from brown algae was higher than the diversity of strains isolated from green and red algae. The commonly isolated species were Penicillium antarcticum, P. bialowiezense, P. brevicompactum, P. crustosum, P. oxalicum, P. rubens, P. sumatrense, and P. terrigenum. While many strains showed endoglucanase, β-glucosidase, and protease activity, no alginase activity was detected. There was a positive correlation between halo-tolerance and endoglucanase activity within Penicillium species. Among 19 Penicillium species, three species-P. kongii, P. olsonii, and P. viticola-have not been previously recorded in Korea.

Rapid Diversity Loss of Competing Animal Species in Well-Connected Landscapes

PubMed Central

Schippers, Peter; Hemerik, Lia; Baveco, Johannes M.; Verboom, Jana

2015-01-01

Population viability of a single species, when evaluated with metapopulation based landscape evaluation tools, always increases when the connectivity of the landscape increases. However, when interactions between species are taken into account, results can differ. We explore this issue using a stochastic spatially explicit meta-community model with 21 competing species in five different competitive settings: (1) weak, coexisting competition, (2) neutral competition, (3) strong, excluding competition, (4) hierarchical competition and (5) random species competition. The species compete in randomly generated landscapes with various fragmentation levels. With this model we study species loss over time. Simulation results show that overall diversity, the species richness in the entire landscape, decreases slowly in fragmented landscapes whereas in well-connected landscapes rapid species losses occur. These results are robust with respect to changing competitive settings, species parameters and spatial configurations. They indicate that optimal landscape configuration for species conservation differs between metapopulation approaches, modelling species separately and meta-community approaches allowing species interactions. The mechanism behind this is that species in well-connected landscapes rapidly outcompete each other. Species that become abundant, by chance or by their completive strength, send out large amounts of dispersers that colonize and take over other patches that are occupied by species that are less abundant. This mechanism causes rapid species loss. In fragmented landscapes the colonization rate is lower, and it is difficult for a new species to establish in an already occupied patch. So, here dominant species cannot easily take over patches occupied by other species and higher diversity is maintained for a longer time. These results suggest that fragmented landscapes have benefits for species conservation previously unrecognized by the landscape ecology

Do the rich get richer? Varying effects of tree species identity and diversity on the richness of understory taxa

USGS Publications Warehouse

Champagne, Juilette; Paine, C. E. Timothy; Schoolmaster, Donald; Stejskal, Robert; Volařík, Daniel; Šebesta, Jan; Trnka, Filip; Koutecký, Tomáš; Švarc, Petr; Svátek, Martin; Hector, Andy; Matula, Radim

2016-01-01

Understory herbs and soil invertebrates play key roles in soil formation and nutrient cycling in forests. Studies suggest that diversity in the canopy and in the understory are positively associated, but these studies often confound the effects of tree species diversity with those of tree species identity and abiotic conditions. We combined extensive field sampling with structural equation modeling to evaluate the simultaneous effects of tree diversity on the species diversity of understory herbs, beetles, and earthworms. The diversity of earthworms and saproxylic beetles was directly and positively associated with tree diversity, presumably because species of both these taxa specialize on certain species of trees. Tree identity also strongly affected diversity in the understory, especially for herbs, likely as a result of interspecific differences in canopy light transmittance or litter decomposition rates. Our results suggest that changes in forest management will disproportionately affect certain understory taxa. For instance, changes in canopy diversity will affect the diversity of earthworms and saproxylic beetles more than changes in tree species composition, whereas the converse would be expected for understory herbs and detritivorous beetles. We conclude that the effects of tree diversity on understory taxa can vary from positive to negative and may affect biogeochemical cycling in temperate forests. Thus, maintaining high diversity in temperate forests can promote the diversity of multiple taxa in the understory.

Do the rich get richer? Varying effects of tree species identity and diversity on the richness of understory taxa.

PubMed

Chamagne, Juliette; Paine, C E Timothy; Schoolmaster, Donald R; Stejskal, Robert; Volarřík, Daniel; Šebesta, Jan; Trnka, Filip; Koutecký, Tomáš; Švarc, Petr; Svátek, Martin; Hector, Andy; Matula, Radim

2016-09-01

Understory herbs and soil invertebrates play key roles in soil formation and nutrient cycling in forests. Studies suggest that diversity in the canopy and in the understory are positively associated, but these studies often confound the effects of tree species diversity with those of tree species identity and abiotic conditions. We combined extensive field sampling with structural equation modeling to evaluate the simultaneous effects of tree diversity on the species diversity of understory herbs, beetles, and earthworms. The diversity of earthworms and saproxylic beetles was directly and positively associated with tree diversity, presumably because species of both these taxa specialize on certain species of trees. Tree identity also strongly affected diversity in the understory, especially for herbs, likely as a result of interspecific differences in canopy light transmittance or litter decomposition rates. Our results suggest that changes in forest management will disproportionately affect certain understory taxa. For instance, changes in canopy diversity will affect the diversity of earthworms and saproxylic beetles more than changes in tree species composition, whereas the converse would be expected for understory herbs and detritivorous beetles. We conclude that the effects of tree diversity on understory taxa can vary from positive to negative and may affect biogeochemical cycling in temperate forests. Thus, maintaining high diversity in temperate forests can promote the diversity of multiple taxa in the understory. © 2016 by the Ecological Society of America.

Ranking Mammal Species for Conservation and the Loss of Both Phylogenetic and Trait Diversity.

PubMed

Redding, David W; Mooers, Arne O

2015-01-01

The 'edge of existence' (EDGE) prioritisation scheme is a new approach to rank species for conservation attention that aims to identify species that are both isolated on the tree of life and at imminent risk of extinction as defined by the World Conservation Union (IUCN). The self-stated benefit of the EDGE system is that it effectively captures unusual 'unique' species, and doing so will preserve the total evolutionary history of a group into the future. Given the EDGE metric was not designed to capture total evolutionary history, we tested this claim. Our analyses show that the total evolutionary history of mammals preserved is indeed much higher if EDGE species are protected than if at-risk species are chosen randomly. More of the total tree is also protected by EDGE species than if solely threat status or solely evolutionary distinctiveness were used for prioritisation. When considering how much trait diversity is captured by IUCN and EDGE prioritisation rankings, interestingly, preserving the highest-ranked EDGE species, or indeed just the most threatened species, captures more total trait diversity compared to sets of randomly-selected at-risk species. These results suggest that, as advertised, EDGE mammal species contribute evolutionary history to the evolutionary tree of mammals non-randomly, and EDGE-style rankings among endangered species can also capture important trait diversity. If this pattern holds for other groups, the EDGE prioritisation scheme has greater potential to be an efficient method to allocate scarce conservation effort.

Genetic diversity and differentiation in reef-building Millepora species, as revealed by cross-species amplification of fifteen novel microsatellite loci.

PubMed

Dubé, Caroline E; Planes, Serge; Zhou, Yuxiang; Berteaux-Lecellier, Véronique; Boissin, Emilie

2017-01-01

Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coral Millepora platyphylla , an important reef-builder of Indo-Pacific reefs . We tested the cross-species amplification of these loci in five other species of the genus Millepora and analysed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target species M. platyphylla, among which twelve were polymorphic with 2-13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five other Millepora species revealed a high probability of amplification success (71%) and polymorphism (59%) of the loci. Our results show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean species M. complanata due to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species of Millepora. Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323-0.496) and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoan Millepora species creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs.

Patterns of orchid bee species diversity and turnover among forested plateaus of central Amazonia

PubMed Central

Machado, Carolina de Barros; Galetti, Pedro Manoel; Oliveira, Marcio; Dirzo, Rodolfo; Fernandes, Geraldo Wilson

2017-01-01

The knowledge of spatial pattern and geographic beta-diversity is of great importance for biodiversity conservation and interpreting ecological information. Tropical forests, especially the Amazon Rainforest, are well known for their high species richness and low similarity in species composition between sites, both at local and regional scales. We aimed to determine the effect and relative importance of area, isolation and climate on species richness and turnover in orchid bee assemblages among plateaus in central Brazilian Amazonia. Variance partitioning techniques were applied to assess the relative effects of spatial and environmental variables on bee species richness, phylogeny and composition. We hypothesized that greater abundance and richness of orchid bees would be found on larger plateaus, with a set of core species occurring on all of them. We also hypothesized that smaller plateaus would possess lower phylogenetic diversity. We found 55 bee species distributed along the nine sampling sites (plateaus) with 17 of them being singletons. There was a significant decrease in species richness with decreasing size of plateaus, and a significant decrease in the similarity in species composition with greater distance and climatic variation among sampling sites. Phylogenetic diversity varied among the sampling sites but was directly related to species richness. Although not significantly related to plateau area, smaller or larger PDFaith were observed in the smallest and the largest plateaus, respectively. PMID:28410432

Patterns of orchid bee species diversity and turnover among forested plateaus of central Amazonia.

PubMed

Antonini, Yasmine; Machado, Carolina de Barros; Galetti, Pedro Manoel; Oliveira, Marcio; Dirzo, Rodolfo; Fernandes, Geraldo Wilson

2017-01-01

The knowledge of spatial pattern and geographic beta-diversity is of great importance for biodiversity conservation and interpreting ecological information. Tropical forests, especially the Amazon Rainforest, are well known for their high species richness and low similarity in species composition between sites, both at local and regional scales. We aimed to determine the effect and relative importance of area, isolation and climate on species richness and turnover in orchid bee assemblages among plateaus in central Brazilian Amazonia. Variance partitioning techniques were applied to assess the relative effects of spatial and environmental variables on bee species richness, phylogeny and composition. We hypothesized that greater abundance and richness of orchid bees would be found on larger plateaus, with a set of core species occurring on all of them. We also hypothesized that smaller plateaus would possess lower phylogenetic diversity. We found 55 bee species distributed along the nine sampling sites (plateaus) with 17 of them being singletons. There was a significant decrease in species richness with decreasing size of plateaus, and a significant decrease in the similarity in species composition with greater distance and climatic variation among sampling sites. Phylogenetic diversity varied among the sampling sites but was directly related to species richness. Although not significantly related to plateau area, smaller or larger PDFaith were observed in the smallest and the largest plateaus, respectively.

Distribution and diversity of twelve Curcuma species in China.

PubMed

Zhang, Lanyue; Wei, Jingwen; Yang, Zhiwen; Chen, Feng; Xian, Qiqiu; Su, Ping; Pan, Wanyi; Zhang, Kun; Zheng, Xi; Du, Zhiyun

2018-02-01

Genus Curcuma a wild species presents an important source of valuable characters for improving the cultivated Curcuma varieties. Based on the collected germplasms, herbariums, field surveys and other literatures, the ecogeographical diversity of Genus Curcuma and its potential distributions under the present and future climate are analysed by DIVA-GIS. The results indicate Genus Curcuma is distributed over 17 provinces in China, and particularly abundant in Guangxi and Guangdong provinces. The simulated current distributions are close to the actual distribution regions. In the future climate, the suitable areas for four Curcuma species will be extended, while for other three species the regions will be significantly decreased, and thus these valuable resources need protecting.

Connecting ground water influxes with fish species diversity in an urbanized watershed

USGS Publications Warehouse

Steffy, L.Y.; McGinty, A.L.; Welty, C.; Kilham, S.S.

2004-01-01

Valley Creek watershed is a small stream system that feeds the Schuylkill River near Philadelphia, Pennsylvania. The watershed is highly urbanized, including over 17 percent impervious surface cover (ISC) by area. Imperviousness in a watershed has been linked to fish community structure and integrity. Generally, above 10 to 12 percent ISC there is marked decline in fish assemblages with fish being absent above 25 percent ISC. This study quantifies the importance of ground water in maintaining fish species diversity in subbasins with over 30 percent ISC. Valley Creek contains an atypical fish assemblage in that the majority of the fish are warm-water species, and the stream supports naturally reproducing brown trout, which were introduced and stocked from the early 1900s to 1985. Fish communities were quantified at 13 stations throughout the watershed, and Simpson's species diversity index was calculated. One hundred and nine springs were located, and their flow rates measured. A cross covariance analysis between Simpson's species diversity index and spring flow rates upstream of fish stations was performed to quantify the spatial correlation between these two variables. The correlation was found to be highest at lag distances up to about 400 m and drop off significantly beyond lag distances of about 800 m.

Direct vs. Microclimate-Driven Effects of Tree Species Diversity on Litter Decomposition in Young Subtropical Forest Stands.

PubMed

Seidelmann, Katrin N; Scherer-Lorenzen, Michael; Niklaus, Pascal A

2016-01-01

Effects of tree species diversity on decomposition can operate via a multitude of mechanism, including alterations of microclimate by the forest canopy. Studying such effects in natural settings is complicated by the fact that topography also affects microclimate and thus decomposition, so that effects of diversity are more difficult to isolate. Here, we quantified decomposition rates of standard litter in young subtropical forest stands, separating effects of canopy tree species richness and topography, and quantifying their direct and micro-climate-mediated components. Our litterbag study was carried out at two experimental sites of a biodiversity-ecosystem functioning field experiment in south-east China (BEF-China). The field sites display strong topographical heterogeneity and were planted with tree communities ranging from monocultures to mixtures of 24 native subtropical tree species. Litter bags filled with senescent leaves of three native tree species were placed from Nov. 2011 to Oct. 2012 on 134 plots along the tree species diversity gradient. Topographic features were measured for all and microclimate in a subset of plots. Stand species richness, topography and microclimate explained important fractions of the variations in litter decomposition rates, with diversity and topographic effects in part mediated by microclimatic changes. Tree stands were 2-3 years old, but nevertheless tree species diversity explained more variation (54.3%) in decomposition than topography (7.7%). Tree species richness slowed litter decomposition, an effect that slightly depended on litter species identity. A large part of the variance in decomposition was explained by tree species composition, with the presence of three tree species playing a significant role. Microclimate explained 31.4% of the variance in decomposition, and was related to lower soil moisture. Within this microclimate effect, species diversity (without composition) explained 8.9% and topography 34.4% of

Direct vs. Microclimate-Driven Effects of Tree Species Diversity on Litter Decomposition in Young Subtropical Forest Stands

PubMed Central

Seidelmann, Katrin N.; Scherer-Lorenzen, Michael; Niklaus, Pascal A.

2016-01-01

Effects of tree species diversity on decomposition can operate via a multitude of mechanism, including alterations of microclimate by the forest canopy. Studying such effects in natural settings is complicated by the fact that topography also affects microclimate and thus decomposition, so that effects of diversity are more difficult to isolate. Here, we quantified decomposition rates of standard litter in young subtropical forest stands, separating effects of canopy tree species richness and topography, and quantifying their direct and micro-climate-mediated components. Our litterbag study was carried out at two experimental sites of a biodiversity-ecosystem functioning field experiment in south-east China (BEF-China). The field sites display strong topographical heterogeneity and were planted with tree communities ranging from monocultures to mixtures of 24 native subtropical tree species. Litter bags filled with senescent leaves of three native tree species were placed from Nov. 2011 to Oct. 2012 on 134 plots along the tree species diversity gradient. Topographic features were measured for all and microclimate in a subset of plots. Stand species richness, topography and microclimate explained important fractions of the variations in litter decomposition rates, with diversity and topographic effects in part mediated by microclimatic changes. Tree stands were 2–3 years old, but nevertheless tree species diversity explained more variation (54.3%) in decomposition than topography (7.7%). Tree species richness slowed litter decomposition, an effect that slightly depended on litter species identity. A large part of the variance in decomposition was explained by tree species composition, with the presence of three tree species playing a significant role. Microclimate explained 31.4% of the variance in decomposition, and was related to lower soil moisture. Within this microclimate effect, species diversity (without composition) explained 8.9% and topography 34.4% of

The roles of community biomass and species pools in the regulation of plant diversity

USGS Publications Warehouse

Grace, J.B.

2001-01-01

Considerable debate has developed over the importance of community biomass and species pools in the regulation of community diversity. Attempts to explain patterns of plant diversity as a function of community biomass or productivity have been only partially successful and in general, have explained only a fraction of the observed variation in diversity. At the same time studies that have focused on the importance of species pools have led some to conclude that diversity is primarily regulated in the short term by the size of the species pool rather than by biotic interactions. In this paper, I explore how community biomass and species pools may work in combination to regulate diversity in herbaceous plant communities. To address this problem, I employ a simple model in which the dynamics of species richness are a function of aboveground community biomass and environmentally controlled gradients in species pools. Model results lead to two main predictions about the role of biomass regulation: (1) Seasonal dynamics of richness will tend to follow a regular oscillation, with richness rising to peak values during the early to middle portion of the growing season and then declining during the latter part of the season. (2.) Seasonal dieback of aboveground tissues facilitates the long-term maintenance of high levels of richness in the community. The persistence of aboveground tissues and accumulation of litter are especially important in limiting the number of species through the suppression of recruitment. Model results also lead to two main predictions about the role of species pools: (1) The height and position of peak richness relative to community biomass will be influenced by the rate at which the species pool increases as available soil resources increase. (2) Variations in nonresource environmental factors (e.g. soil pH or soil salinity) have the potential to regulate species pools in a way that is uncorrelated with aboveground biomass. Under extreme conditions

Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems

NASA Astrophysics Data System (ADS)

Maslov, Sergei; Sneppen, Kim

2017-01-01

Determinants of species diversity in microbial ecosystems remain poorly understood. Bacteriophages are believed to increase the diversity by the virtue of Kill-the-Winner infection bias preventing the fastest growing organism from taking over the community. Phage-bacterial ecosystems are traditionally described in terms of the static equilibrium state of Lotka-Volterra equations in which bacterial growth is exactly balanced by losses due to phage predation. Here we consider a more dynamic scenario in which phage infections give rise to abrupt and severe collapses of bacterial populations whenever they become sufficiently large. As a consequence, each bacterial population in our model follows cyclic dynamics of exponential growth interrupted by sudden declines. The total population of all species fluctuates around the carrying capacity of the environment, making these cycles cryptic. While a subset of the slowest growing species in our model is always driven towards extinction, in general the overall ecosystem diversity remains high. The number of surviving species is inversely proportional to the variation in their growth rates but increases with the frequency and severity of phage-induced collapses. Thus counter-intuitively we predict that microbial communities exposed to more violent perturbations should have higher diversity.

Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems

PubMed Central

Maslov, Sergei; Sneppen, Kim

2017-01-01

Determinants of species diversity in microbial ecosystems remain poorly understood. Bacteriophages are believed to increase the diversity by the virtue of Kill-the-Winner infection bias preventing the fastest growing organism from taking over the community. Phage-bacterial ecosystems are traditionally described in terms of the static equilibrium state of Lotka-Volterra equations in which bacterial growth is exactly balanced by losses due to phage predation. Here we consider a more dynamic scenario in which phage infections give rise to abrupt and severe collapses of bacterial populations whenever they become sufficiently large. As a consequence, each bacterial population in our model follows cyclic dynamics of exponential growth interrupted by sudden declines. The total population of all species fluctuates around the carrying capacity of the environment, making these cycles cryptic. While a subset of the slowest growing species in our model is always driven towards extinction, in general the overall ecosystem diversity remains high. The number of surviving species is inversely proportional to the variation in their growth rates but increases with the frequency and severity of phage-induced collapses. Thus counter-intuitively we predict that microbial communities exposed to more violent perturbations should have higher diversity. PMID:28051127

Phylogenetic study of the Colletotrichum species on imported citrus fruits uncovers a low diversity and a new species in the Colletotrichum gigasporum complex.

PubMed

Douanla-Meli, Clovis; Unger, Jens-Georg

2017-10-01

Colletotrichum species associated with citrus fruits are fragmentarily known and it lacks accordingly accurate information on the diversity carried alongside the trade of these commodities from producer countries to Europe. In this study, we investigated the molecular phylogenetic diversity, colonisation, and prevalence of Colletotrichum isolated from asymptomatic and diseased tissues of nine citrus fruit species from 17 geographically diverse countries. Totally 454 isolates were morphoculturally characterised, and multilocus analyses (ACT, ApMat, CHS-1, GAPDH, ITS, TUB2) was performed on a subset of representative morphotype isolates. Results led to the identification of three previously known species (Colletotrichum gloeosporioides, Colletotrichum karstii, Colletotrichum siamense) and one novel lineage comprising endophytic isolates from Citrus maxima. Based on this lineage, Colletotrichum citri-maximae is described as a new species in the Colletotrichum gigasporum complex, and is characterised by a long deletion in the GAPDH sequence, a character shared with three of its phylogenetic sister taxa. Prevalence of Colletotrichum varied among citrus species and was greatest on Citrus sinensis fruits. C. gloeosporioides was the most common species followed by C. siamense. Except for the new species, all other isolated Colletotrichum spp. also colonise citrus leaves, but the overall diversity on fruits may be lower than that of leaves. Copyright © 2017 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Indicator 1.08. Population levels of selected representative forest-associated species to describe genetic diversity

Treesearch

C. H. Sieg; S. M. Owen; C. H. Flather

2011-01-01

This indicator uses population trends of selected bird and tree species as a surrogate measure of genetic diversity. Population decreases, especially associated with small populations, can lead to decreases in genetic diversity, and contribute to increased risk of extinction. Many forest-associated species rely on some particular forest structure, vegetation...

Phytoplankton species diversity indices in Anjanapura reservoir, Western Ghat region, India.

PubMed

Basavaraja, D; Narayana, J; Puttaiah, E T; Prakash, K

2013-07-01

A qualitative study on species composition and diversity of phytoplankton flora was carried out in the Anjanapura reservoir. Water samples were collected monthly at four sites from November 2005 to October 2007 for plankton analysis. A total of 152 phytoplankton species belonging to 59 genera were recorded. The species belonging to genera Crucigenia, Pediastrum, Scenedesmus, Tetraedron, Cyclotella, Gyrosigma, Melosira, Navicula, Fragillaria, pinnularia, Synedra, Closterium, Cosmarium, Euastrum, Staurastrum, Gleocapsa, Merismopedia, Microcystis, Oscillatoria, Euglena and Phacus were found dominant. Phytoplankton density was recorded in the range of 222-1467 Org l(-1) for chlorococcales, 267-1467 Org I (-1) for diatoms, 44-889 Org l(-1) for desmids, 44-889 Org l(-1) for blue-greens and 22-1667 Org l(-1) for euglenoids. Seasonal density Shannon-Weiner diversity index (1.60-1.88) indicate that reservoir exhibited rich phytoplankton and Nygaard tropic status indices for myxophycean (1.0-1.50), chlorophycean (1.62-2.16), diatoms (0.10-0.14), euglenophycean (0.18-0.19) and compound quotient(3.25-4.66) showed that reservoir was moderately polluted. From the observed data, it could be concluded that the presence of more diverse group of phytoplankton indicate the productivity of the reservoir.

Detection of Helicobacter pylori and fecal indicator bacteria in five North American rivers.

USGS Publications Warehouse

Voytek, M.A.; Ashen, J.B.; Fogarty, L.R.; Kirshtein, J.D.; Landa, E.R.

2005-01-01

This study examines the use of fecal indicator bacteria (FIB) as a predictor of the presence of Helicobacter spp. A combination of standard culture and molecular techniques were used to detect and quantify FIB, Helicobacter spp. and H. pylori from five North American rivers of different size and with different land use characteristics. Primers designed to amplify genes specific to Helicobacter spp. and H. pylori were evaluated for their efficacy in detection and quantification in environmental samples. Helicobacter spp. were detected in 18/33 (55%) of river samples. H. pylori was detected in 11/33 (33%) of river samples. FIB were found in 32/33 (96%) of river samples. When FIB abundance exceeded USEPA water quality standards for single samples, Helicobacter or H. pylori were detected in 7/15 (47%) cases. No numerical correlation was found between the presence of FIB and either Helicobacter spp. or H. pylori. This suggests that the presence of FIB will be of limited use for detection of Helicobacter spp. or H. pylori by public health agencies.

Species diversity of polyporoid and corticioid fungi in northern hardwood forests with differing management histories.

PubMed

Lindner, Daniel L; Burdsall, Harold H; Stanosz, Glen R

2006-01-01

Effects of forest management on fungal diversity were investigated by sampling fruit bodies of polyporoid and corticioid fungi in forest stands that have different management histories. Fruit bodies were sampled in 15 northern hardwood stands in northern Wisconsin and the upper peninsula of Michigan. Sampling was conducted in five old-growth stands, five uneven-age stands, three even-age unthinned stands and two even-age thinned stands. Plots 100 m x 60 m were established and 3000 m2 within each plot was sampled during the summers of 1996 and 1997. A total of 255 polyporoid and corticioid morphological species were identified, 46 (18%) of which could not be assigned to a described species. Species accumulation curves for sites and management classes differed from straight lines, although variability from year to year suggests that more than 2 y of sampling are needed to characterize annual variation. Mean species richness and diversity index values did not vary significantly by management class, although mean richness on large diameter wood (> or = 15 cm diam) varied with moderate significance. Richness values on small diameter debris varied significantly by year, indicating that a large part of year-to-year variability in total species richness is due to small diameter debris. Ten species had abundance levels that varied by management class. Two of these species. Changes in the diversity and species composition of the wood-inhabiting fungal community could have significant implications for the diversity, health and productivity of forest ecosystems.

Fire alters patterns of genetic diversity among 3 lizard species in Florida Scrub habitat.

PubMed

Schrey, Aaron W; Ashton, Kyle G; Heath, Stacy; McCoy, Earl D; Mushinsky, Henry R

2011-01-01

The Florida Sand Skink (Plestiodon reynoldsi), the Florida Scrub Lizard (Sceloporus woodi), and the Six-lined Racerunner (Aspidoscelis sexlineata) occur in the threatened and fire-maintained Florida scrub habitat. Fire may have different consequences to local genetic diversity of these species because they each have different microhabitat preference. We collected tissue samples of each species from 3 sites with different time-since-fire: Florida Sand Skink n = 73, Florida Scrub Lizard n = 70, and Six-lined Racerunner n = 66. We compared the effect of fire on genetic diversity at microsatellite loci for each species. We screened 8 loci for the Florida Sand Skink, 6 loci for the Florida Scrub Lizard, and 6 loci for the Six-lined Racerunner. We also tested 2 potential driving mechanisms for the observed change in genetic diversity, a metapopulation source/sink model and a local demographic model. Genetic diversity varied with fire history, and significant genetic differentiation occurred among sites. The Florida Scrub Lizard had highest genetic variation at more recently burned sites, whereas the Florida Sand Skink and the Six-lined Racerunner had highest genetic variation at less recently burned sites. Habitat preferences of the Florida Sand Skink and the Florida Scrub Lizard may explain their discordant results, and the Six-lined Racerunner may have a more complicated genetic response to fire or is acted on at a different geographic scale than we have investigated. Our results indicate that these species may respond to fire in a more complicated manner than predicted by our metapopulation model or local demographic model. Our results show that the population-level responses in genetic diversity to fire are species-specific mandating conservation management of habitat diversity through a mosaic of burn frequencies.

Tree Species Richness Promotes Invertebrate Herbivory on Congeneric Native and Exotic Tree Saplings in a Young Diversity Experiment.

PubMed

Wein, Annika; Bauhus, Jürgen; Bilodeau-Gauthier, Simon; Scherer-Lorenzen, Michael; Nock, Charles; Staab, Michael

2016-01-01

Tree diversity in forests is an important driver of ecological processes including herbivory. Empirical evidence suggests both negative and positive effects of tree diversity on herbivory, which can be, respectively, attributed to associational resistance or associational susceptibility. Tree diversity experiments allow testing for associational effects, but evidence regarding which pattern predominates is mixed. Furthermore, it is unknown if herbivory on tree species of native vs. exotic origin is influenced by changing tree diversity in a similar way, or if exotic tree species escape natural enemies, resulting in lower damage that is unrelated to tree diversity. To address these questions, we established a young tree diversity experiment in temperate southwestern Germany that uses high planting density (49 trees per plot; plot size 13 m2). The species pool consists of six congeneric species pairs of European and North American origin (12 species in total) planted in monocultures and mixtures (1, 2, 4, 6 species). We assessed leaf damage by leaf-chewing insects on more than 5,000 saplings of six broadleaved tree species. Plot-level tree species richness increased leaf damage, which more than doubled from monocultures to six-species mixtures, strongly supporting associational susceptibility. However, leaf damage among congeneric native and exotic species pairs was similar. There were marked differences in patterns of leaf damage across tree genera, and only the genera likely having a predominately generalist herbivore community showed associational susceptibility, irrespective of the geographical origin of a tree species. In conclusion, an increase in tree species richness in young temperate forests may result in associational susceptibility to feeding by generalist herbivores.

Diversity of Helicobacter pylori genotypes in Iranian patients with different gastroduodenal disorders

PubMed Central

Vaziri, Farzam; Najar Peerayeh, Shahin; Alebouyeh, Masoud; Mirzaei, Tabassom; Yamaoka, Yoshio; Molaei, Mahsa; Maghsoudi, Nader; Zali, Mohammad Reza

2013-01-01

AIM: To investigate the diversity of Helicobacter pylori (H. pylori) genotypes and correlations with disease outcomes in an Iranian population with different gastroduodenal disorders. METHODS: Isolates of H. pylori from patients with different gastroduodenal disorders were analyzed after culture and identification by phenotypic and genotypic methods. Genomic DNA was extracted with the QIAamp DNA mini kit (Qiagen, Germany). After DNA extraction, genotyping was done for cagA, vacA (s and m regions), iceA (iceA1, iceA2) and babA with specific primers for each allele using polymerase chain reaction (PCR). All patients’ pathologic and clinical data and their relation with known genotypes were analyzed by using SPSS version 19.0 software. χ2 test and Fisher’s exact test were used to assess relationships between categorical variables. The level of statistical significance was set at P < 0.05. RESULTS: A total of 71 isolates from 177 patients with different gastroduodenal disorders were obtained. Based on analysis of the cagA gene (positive or negative), vacA s-region (s1 or s2), vacA m-region (m1 or m2), iceA allelic type (iceA1 and iceA2) and babA gene (positive or negative), twenty different genotypic combinations were recognized. The prevalence of cagA, vacA s1, vacA s2, vacA m1, vacA m2, iceA1, iceA2, iceA1+iceA2 and babA were 62%, 78.9%, 19.7%, 21.1%, 78.9%, 15.5%, 22.5%, 40.8% and 95.8%, respectively. Interestingly, evaluation of PCR results for cagA in 6 patients showed simultaneous existence of cagA variants according to their size diversities that proposed mixed infection in these patients. The most prevalent genotype in cagA-positive isolates was cagA+/vacAs1m2/iceA1+A2/babA+ and in cagA-negative isolates was cagA-/vacAs1m2/iceA-/babA+. There were no relationships between the studied genes and histopathological findings (H. pylori density, neutrophil activity, lymphoid aggregation in lamina propria and glandular atrophy). The strains which carry cagA, vac

Spectral distance decay: Assessing species beta-diversity by quantile regression

USGS Publications Warehouse

Rocchinl, D.; Nagendra, H.; Ghate, R.; Cade, B.S.

2009-01-01

Remotely sensed data represents key information for characterizing and estimating biodiversity. Spectral distance among sites has proven to be a powerful approach for detecting species composition variability. Regression analysis of species similarity versus spectral distance may allow us to quantitatively estimate how beta-diversity in species changes with respect to spectral and ecological variability. In classical regression analysis, the residual sum of squares is minimized for the mean of the dependent variable distribution. However, many ecological datasets are characterized by a high number of zeroes that can add noise to the regression model. Quantile regression can be used to evaluate trend in the upper quantiles rather than a mean trend across the whole distribution of the dependent variable. In this paper, we used ordinary least square (ols) and quantile regression to estimate the decay of species similarity versus spectral distance. The achieved decay rates were statistically nonzero (p < 0.05) considering both ols and quantile regression. Nonetheless, ols regression estimate of mean decay rate was only half the decay rate indicated by the upper quantiles. Moreover, the intercept value, representing the similarity reached when spectral distance approaches zero, was very low compared with the intercepts of upper quantiles, which detected high species similarity when habitats are more similar. In this paper we demonstrated the power of using quantile regressions applied to spectral distance decay in order to reveal species diversity patterns otherwise lost or underestimated by ordinary least square regression. ?? 2009 American Society for Photogrammetry and Remote Sensing.

Environmental diversity as a surrogate for species representation.

PubMed

Beier, Paul; de Albuquerque, Fábio Suzart

2015-10-01

Because many species have not been described and most species ranges have not been mapped, conservation planners often use surrogates for conservation planning, but evidence for surrogate effectiveness is weak. Surrogates are well-mapped features such as soil types, landforms, occurrences of an easily observed taxon (discrete surrogates), and well-mapped environmental conditions (continuous surrogate). In the context of reserve selection, the idea is that a set of sites selected to span diversity in the surrogate will efficiently represent most species. Environmental diversity (ED) is a rarely used surrogate that selects sites to efficiently span multivariate ordination space. Because it selects across continuous environmental space, ED should perform better than discrete surrogates (which necessarily ignore within-bin and between-bin heterogeneity). Despite this theoretical advantage, ED appears to have performed poorly in previous tests of its ability to identify 50 × 50 km cells that represented vertebrates in Western Europe. Using an improved implementation of ED, we retested ED on Western European birds, mammals, reptiles, amphibians, and combined terrestrial vertebrates. We also tested ED on data sets for plants of Zimbabwe, birds of Spain, and birds of Arizona (United States). Sites selected using ED represented European mammals no better than randomly selected cells, but they represented species in the other 7 data sets with 20% to 84% effectiveness. This far exceeds the performance in previous tests of ED, and exceeds the performance of most discrete surrogates. We believe ED performed poorly in previous tests because those tests considered only a few candidate explanatory variables and used suboptimal forms of ED's selection algorithm. We suggest future work on ED focus on analyses at finer grain sizes more relevant to conservation decisions, explore the effect of selecting the explanatory variables most associated with species turnover, and investigate

Tree diversity and species identity effects on soil fungi, protists and animals are context dependent.

PubMed

Tedersoo, Leho; Bahram, Mohammad; Cajthaml, Tomáš; Põlme, Sergei; Hiiesalu, Indrek; Anslan, Sten; Harend, Helery; Buegger, Franz; Pritsch, Karin; Koricheva, Julia; Abarenkov, Kessy

2016-02-01

Plant species richness and the presence of certain influential species (sampling effect) drive the stability and functionality of ecosystems as well as primary production and biomass of consumers. However, little is known about these floristic effects on richness and community composition of soil biota in forest habitats owing to methodological constraints. We developed a DNA metabarcoding approach to identify the major eukaryote groups directly from soil with roughly species-level resolution. Using this method, we examined the effects of tree diversity and individual tree species on soil microbial biomass and taxonomic richness of soil biota in two experimental study systems in Finland and Estonia and accounted for edaphic variables and spatial autocorrelation. Our analyses revealed that the effects of tree diversity and individual species on soil biota are largely context dependent. Multiple regression and structural equation modelling suggested that biomass, soil pH, nutrients and tree species directly affect richness of different taxonomic groups. The community composition of most soil organisms was strongly correlated due to similar response to environmental predictors rather than causal relationships. On a local scale, soil resources and tree species have stronger effect on diversity of soil biota than tree species richness per se.

Mosquito Species (Diptera: Culicidae) Diversity from Ovitraps in a Mesoamerican Tropical Rainforest.

PubMed

Chaverri, Luis Guillermo; Dillenbeck, Claire; Lewis, Devon; Rivera, Cindy; Romero, Luis Mario; Chaves, Luis Fernando

2018-05-04

Mosquito sampling using efficient traps that can assess species diversity and/or presence of dominant vectors is important for understanding the entomological risk of mosquito-borne disease transmission. Here, we present results from a survey of mosquito species sampled with ovitraps in a neotropical rainforest of Costa Rica. We found the method to be an efficient sampling tool. With a total sampling effort of 29 traps, we collected 157 fourth-instar larvae and three pupae belonging to eight mosquito taxonomic units (seven species and individuals from a homogenous taxonomic unit identified to the genus level). In our samples, we found two medically important species, Sabethes chloropterus (Humboldt) and Trichoprosopon digitatum (Rondani). The former is a proven vector of Yellow Fever in sylvatic environments and the later has been found infected with several arboviruses. We also found that mosquito species abundance and diversity increased with canopy cover and in environments where leaf litter dominated the ground cover. Finally, our results suggest that ovitraps have a great potential for systematic sampling in longitudinal and cross-sectional ecological "semi-field" studies in neotropical settings.

Unrecognized coral species diversity masks differences in functional ecology

PubMed Central

Boulay, Jennifer N.; Hellberg, Michael E.; Cortés, Jorge; Baums, Iliana B.

2014-01-01

Porites corals are foundation species on Pacific reefs but a confused taxonomy hinders understanding of their ecosystem function and responses to climate change. Here, we show that what has been considered a single species in the eastern tropical Pacific, Porites lobata, includes a morphologically similar yet ecologically distinct species, Porites evermanni. While P. lobata reproduces mainly sexually, P. evermanni dominates in areas where triggerfish prey on bioeroding mussels living within the coral skeleton, thereby generating asexual coral fragments. These fragments proliferate in marginal habitat not colonized by P. lobata. The two Porites species also show a differential bleaching response despite hosting the same dominant symbiont subclade. Thus, hidden diversity within these reef-builders has until now obscured differences in trophic interactions, reproductive dynamics and bleaching susceptibility, indicative of differential responses when confronted with future climate change. PMID:24335977

Unrecognized coral species diversity masks differences in functional ecology.

PubMed

Boulay, Jennifer N; Hellberg, Michael E; Cortés, Jorge; Baums, Iliana B

2014-02-07

Porites corals are foundation species on Pacific reefs but a confused taxonomy hinders understanding of their ecosystem function and responses to climate change. Here, we show that what has been considered a single species in the eastern tropical Pacific, Porites lobata, includes a morphologically similar yet ecologically distinct species, Porites evermanni. While P. lobata reproduces mainly sexually, P. evermanni dominates in areas where triggerfish prey on bioeroding mussels living within the coral skeleton, thereby generating asexual coral fragments. These fragments proliferate in marginal habitat not colonized by P. lobata. The two Porites species also show a differential bleaching response despite hosting the same dominant symbiont subclade. Thus, hidden diversity within these reef-builders has until now obscured differences in trophic interactions, reproductive dynamics and bleaching susceptibility, indicative of differential responses when confronted with future climate change.

Genetic diversity and population structure of an extremely endangered species: the world's largest Rhododendron.