scholarly journals Trophic and symbiotic links between obligate-glacier water bears (Tardigrada) and cryoconite microorganisms

PLoS ONE ◽  
2022 ◽  
Vol 17 (1) ◽  
pp. e0262039
Author(s):  
Krzysztof Zawierucha ◽  
Artur Trzebny ◽  
Jakub Buda ◽  
Elizabeth Bagshaw ◽  
Andrea Franzetti ◽  
...  
Keyword(s):  
Relative Number ◽  
Shannon Index ◽  
Ecosystem Functions ◽  
Host Group ◽  
Operational Taxonomic Units ◽  
Microbial Group ◽  
Indicator Analysis ◽  
Trophic Webs ◽  
First Time ◽  
Water Bears

Insights into biodiversity and trophic webs are important for understanding ecosystem functions. Although the surfaces of glaciers are one of the most productive and biologically diverse parts of the cryosphere, the links between top consumers, their diet and microbial communities are poorly understood. In this study, for the first time we investigated the relationships between bacteria, fungi and other microeukaryotes as they relate to tardigrades, microscopic metazoans that are top consumers in cryoconite, a biologically rich and productive biogenic sediment found on glacier surfaces. Using metabarcoding (16S rDNA for bacteria, ITS1 for fungi, and 18S rDNA for other microeukaryotes), we analyzed the microbial community structures of cryoconite and compared them with the community found in both fully fed and starved tardigrades. The community structure of each microbial group (bacteria, fungi, microeukaryotes) were similar within each host group (cryoconite, fully fed tardigrades and starved tardigrades), and differed significantly between groups, as indicated by redundancy analyses. The relative number of operational taxonomic units (ZOTUs, OTUs) and the Shannon index differed significantly between cryoconite and tardigrades. Species indicator analysis highlighted a group of microbial taxa typical of both fully fed and starved tardigrades (potential commensals), like the bacteria of the genera Staphylococcus and Stenotrophomonas, as well as a group of taxa typical of both cryoconite and fully fed tardigrades (likely part of the tardigrade diet; bacteria Flavobacterium sp., fungi Preussia sp., algae Trebouxiophyceae sp.). Tardigrades are consumers of bacteria, fungi and other microeukaryotes in cryoconite and, being hosts for diverse microbes, their presence can enrich the microbiome of glaciers.

Exploring the plant environmental DNA diversity in soil from two sites on Deception Island (Antarctica, South Shetland Islands) using metabarcoding

2021 ◽  
pp. 1-10
Author(s):  
Micheline Carvalho-Silva ◽  
Luiz Henrique Rosa ◽  
Otávio H.B. Pinto ◽  
Thamar Holanda Da Silva ◽  
Diego Knop Henriques ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Crater Lake ◽  
Environmental Dna ◽  
Food Sources ◽  
South Shetland Islands ◽  
Deception Island ◽  
Shetland Islands ◽  
Operational Taxonomic Units ◽  
First Time ◽  
Impacted Site

Abstract The few Antarctic studies to date to have applied metabarcoding in Antarctica have primarily focused on microorganisms. In this study, for the first time, we apply high-throughput sequencing of environmental DNA to investigate the diversity of Embryophyta (Viridiplantae) DNA present in soil samples from two contrasting locations on Deception Island. The first was a relatively undisturbed site within an Antarctic Specially Protected Area at Crater Lake, and the second was a heavily human-impacted site in Whalers Bay. In samples obtained at Crater Lake, 84% of DNA reads represented fungi, 14% represented Chlorophyta and 2% represented Streptophyta, while at Whalers Bay, 79% of reads represented fungi, 20% represented Chlorophyta and < 1% represented Streptophyta, with ~1% of reads being unassigned. Among the Embryophyta we found 16 plant operational taxonomic units from three Divisions, including one Marchantiophyta, eight Bryophyta and seven Magnoliophyta. Sequences of six taxa were detected at both sampling sites, eight only at Whalers Bay and two only at Crater Lake. All of the Magnoliophyta sequences (flowering plants) represent species that are exotic to Antarctica, with most being plausibly linked to human food sources originating from local national research operator and tourism facilities.

scholarly journals Molecular diversity of bacteria in commercially available “Spirulina” food supplements

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1610 ◽  
Author(s):  
Elisabeth Vardaka ◽  
Konstantinos A. Kormas ◽  
Matina Katsiapi ◽  
Savvas Genitsaris ◽  
Maria Moustaka-Gouni
Keyword(s):  
Natural Product ◽  
454 Pyrosequencing ◽  
Molecular Diversity ◽  
Arthrospira Platensis ◽  
Food Supplements ◽  
Health Issues ◽  
Operational Taxonomic Units ◽  
Health Promoting ◽  
First Time ◽  
Pyrosequencing Analysis

The cyanobacteriumArthrospirais among the most well-known food supplements worldwide known as “Spirulina.” While it is a widely recognized health-promoting natural product, there are no reports on the molecular diversity of commercially available brands of “Spirulina” supplements and the occurrence of other cyanobacterial and heterotrophic bacterial microorganisms in these products. In this study, 454-pyrosequencing analysis of the total bacterial occurrence in 31 brands of “Spirulina” dietary supplements from the Greek market was applied for the first time. In all samples, operational taxonomic units (OTUs) ofArthrospira platensiswere the predominant cyanobacteria. Some products contained additional cyanobacterial OTUs including a few known potentially toxic taxa. Moreover, 469 OTUs were detected in all 31 products collectively, with most of them being related to the Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Verrucomicrobia. All samples included heterotrophic bacterial OTUs, ranging from 9–157 per product. Among the most common OTUs were ones closely related to taxa known for causing health issues (i.e.,Pseudomonas,Flavobacterium,Vibrio,Aeromonas,Clostridium,Bacillus,Fusobacterium,Enterococcus). The observed high cyanobacterial and heterotrophic bacterial OTUs richness in the final product is a point for further research on the growth and processing ofArthrospirabiomass for commercial purposes.

scholarly journals Late Pleistocene and Holocene small mammal (Lipotyphla, Rodentia, Lagomorpha) remains from Medvezhyi Klyk Cave in the Southern Russian Far East

2020 ◽  
Vol 324 (1) ◽  
pp. 124-145 ◽  
Author(s):  
V.E. Omelko ◽  
Y.V. Kuzmin ◽  
M.P. Tiunov ◽  
L.L. Voyta ◽  
G.S. Burr
Keyword(s):  
Late Pleistocene ◽  
Russian Far East ◽  
Far East ◽  
Relative Number ◽  
Taxonomic Diversity ◽  
14C Dating ◽  
Faunal Complexes ◽  
Extinct Genus ◽  
High Degree ◽  
First Time

Late Pleistocene-Holocene faunal complexes of small mammals (Lipotyphla, Rodentia, and Lagomorpha) from the Russian Far East are described for the first time. We used material from the Medvezhyi Klyk Cave, located in Southern Sikhote-Alin. The numerous fossil findings from the cave display a remarkable taxonomic diversity and high degree of preservation. AMS 14C dating used for determination of deposits age. The Holocene sediments were divided into three periods: Early, Middle, and Late. The Pleistocene deposits age was not exactly determined, but under approximately estimation it can reach 50–60 ka. Thirty-nine species were found, including one member of the extinct genus of arvicolins. There are six faunal complexes identified from the studied Late Pleistocene and Holocene deposits. In general, the faunal complexes characterized by the dominance of Craseomys rufocanus within rodents, Sorex caecutiens within lipotyphlans; and relatively stability composition of most number of the dominant, codominant and subdominant species. Accordingly, the faunal complexes were described by means of two determining criteria only: relative number of species; and presence or absence of certain species. The dominant species are eurytopic and so they cannot use for reconstruction of the paleoenvironment.

scholarly journals Identification of arbuscular mycorrhizal fungi in soils of the North Caucasus based on Illumina MiSeq data for ITS1 and ITS2 regions

2020 ◽  
Vol 23 ◽  
pp. 02013
Author(s):  
Andrey P. Yurkov ◽  
Alexey A. Kryukov ◽  
Anastasia O. Gorbunova ◽  
Andrey V. Shcherbakov ◽  
Peter M. Zhurbenko
Keyword(s):  
Sample Preparation ◽  
Arbuscular Mycorrhizal Fungi ◽  
Mycorrhizal Fungi ◽  
Arbuscular Mycorrhizal ◽  
Illumina Miseq ◽  
North Caucasus ◽  
Operational Taxonomic Units ◽  
The North ◽  
First Time ◽  
Its1 And Its2

The objective of our research was to analyze the efficiency of identification of arbuscular mycorrhizal fungi (AMF) for 2 regions: ITS1 and ITS2 regions of AMF DNA isolated from the soils of the North Caucasus (Karachay-Cherkessia). For the first time the necessity of different AMF species identification using both ITS regions was revealed, but not one region. The research demonstrated: 1) the set of taxa is different using ITS1- and ITS2-based identification; 2) analysis of the ITS1 region reveals a greater number of operational taxonomic units; 3) ITS2 allows identification of AMF at the species level more often. Sample preparation for Illumina MiSeq analysis was optimized. Obligatory stages in the sample preparation were the purification of DNA in the agarose gel in Silica after isolation, as well as separate amplification of ITS1 and ITS2 followed by combining and joint sequencing for each sample. The results showed the highest AMF biodiversity for the 176Te sample from the ecosystem of the subalpine meadow of the southeastern slope of Malaya Hatipara mountain (43°25′48.0″N 41°42′31.0″E; 2401 m above sea level), in which 8 species of AMF were identified (Archaeospora spainiae, Claroideoglomus claroideum, Diversispora versiformis, Entrophpora infrequens, Funneliformis mosseae, Glomus indicum, Paraglomus laccatum, Rhizophagus irregularis).

scholarly journals Seasonal Diversity of Endophytic Bacteria Associated with Cinnamomum camphora (L.) Presl.

Diversity ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 112 ◽  
Author(s):  
Abubakr Abdelwhab Hamd Elmagzob ◽  
Muhammed Mustapha Ibrahim ◽  
Guo-Fang Zhang
Keyword(s):  
16S Rdna ◽  
High Throughput Sequencing ◽  
Shannon Index ◽  
Ribosomal Database Project ◽  
Cinnamomum Camphora ◽  
Operational Taxonomic Units ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Endophytic Bacterial Community ◽  
Seasonal Diversity

Investigations on the density, diversity, and distribution of endophytic bacterial community associated with leaves of Cinnamomum camphora (L.) Presl. were carried out during three seasons using 16s rDNA high-throughput sequencing technology. Samples were collected from five species in Nanping (A, B, C, D, and E) and one from Fuqin (F) in the Fujian province, China in the months of April, July, and October (represented by 1, 2 and 3), indicating spring, summer, and early winter, respectively. Results from 16s rDNA sequences revealed 10,844,124 effective sequences. The highest OTUs (Operational taxonomic units) was highest in the A1 sample (1086), while the lowest was in C2 (509). Our observations showed that samples taken in October had the highest diversity of endophytes as indicated by the Shannon index (B3 = 5.3337), Chao1 (E3 = 1233.10), abundance-based coverage estimator (ACE) (A3 = 1764.72), and the Simpson indices of diversity (C3 = 0.1655) irrespective of the species. The order of the endophytes richness in the samples was April > July > October. The Ribosomal Database Project (RDP) classifier showed that the obtained sequences belonged to nine major phyla: Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Acidobacteria, Planctomycetes, Chloroflexi, and Fusobacteria. Proteobacteria accounted for the highest proportion in each sample, ranging from 35.15% to 89.72%. These sequences belonged mainly to 10 orders: Rhizobiales, Clostridiales, Peseudomonadales, Burkholderiales, Bacteroidales, Enterobacteriales, Rhodocyclales, Sphingomonadales, Lactobacillales, and Bacillales. Also, other taxa with possible taxonomic statuses, which were unclassified, were present.

scholarly journals Faunistic analyses of fruit fly species (Diptera: Tephritidae) in orchards surrounded by Atlantic Forest fragments in the metropolitan region of Curitiba, Paraná state, Brazil

2019 ◽  
Vol 79 (3) ◽  
pp. 395-403 ◽  
Author(s):  
L. B. Monteiro ◽  
J. A. S. Tomba ◽  
G. Nishimura ◽  
R. S. Monteiro ◽  
E. Foelkel ◽  
...  
Keyword(s):  
Plant Protection ◽  
Crop Protection ◽  
Fruit Fly ◽  
Fruit Flies ◽  
Shannon Index ◽  
Metropolitan Region ◽  
Forest Fragments ◽  
Explanatory Variables ◽  
Peach Trees ◽  
First Time

Abstract The objective of this trial was to characterize the assemblage structure of fruit flies (Diptera: Tephritidae) by determining the diversity and faunal indices. Fruit flies were collected for ten years between 2003 and 2015 in six municipalities of the Metropolitan Region of Curitiba, Paraná. The orchards were divided into three crop protection strategies: organic, conventional, and integrated pest management. The characteristic of each community was determined using the Shannon-Wiener, Margalef, and Pielou’s indexes. The frequency, constancy, and dominance indexes were also determined. Biological material was analyzed using the explanatory variables: site, crop, plant protection strategy, and susceptibility period. A total of 8,089 fruit flies were collected, of which 4,681 were females. The species Anastrepha daciformis Bezzi, A. dissimilis Stone, A. distincta Greene and A. pickeli Lima were recorded for the first time in Paraná State, the occurrence of three other species was recorded for the first time in the Metropolitan Region of Curitiba (A. montei Lima, A. obliqua Macquart, and A. sororcula Zucchi), in addition A. fraterculus (Wiedemann), A. grandis (Macquart) and Ceratitis capitata (Wiedemann). A. fraterculus accounted for 98.5% of the collected species. Only A. fraterculus and A. sororcula were found in fruits. Fruit flies occurred predominantly in peach trees cultivated under organic conditions. The Shannon index indicated that the municipality of Cerro Azul had the highest diversity and richness whereas apple orchards had the lowest diversity. Crops cultivated under organic conditions exhibited the highest diversity whereas those cultivated under conventional conditions had the highest evenness index. The largest specimens number was collected during the period of crop susceptibility.

Europe-Wide Dampening of Population Cycles in Keystone Herbivores

Science ◽  
2013 ◽  
Vol 340 (6128) ◽  
pp. 63-66 ◽  
Author(s):  
Thomas Cornulier ◽  
Nigel G. Yoccoz ◽  
Vincent Bretagnolle ◽  
Jon E. Brommer ◽  
Alain Butet ◽  
...  
Keyword(s):  
Environmental Changes ◽  
Population Cycles ◽  
Ecosystem Functions ◽  
Population Fluctuations ◽  
Regulatory Processes ◽  
Cycle Amplitude ◽  
Vole Species ◽  
Low Amplitude ◽  
Trophic Webs ◽  
Winter Population

Suggestions of collapse in small herbivore cycles since the 1980s have raised concerns about the loss of essential ecosystem functions. Whether such phenomena are general and result from extrinsic environmental changes or from intrinsic process stochasticity is currently unknown. Using a large compilation of time series of vole abundances, we demonstrate consistent cycle amplitude dampening associated with a reduction in winter population growth, although regulatory processes responsible for cyclicity have not been lost. The underlying syndrome of change throughout Europe and grass-eating vole species suggests a common climatic driver. Increasing intervals of low-amplitude small herbivore population fluctuations are expected in the future, and these may have cascading impacts on trophic webs across ecosystems.

scholarly journals Effect of formaldehyde exposure on bacterial communities in simulating indoor environments

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jianguo Guo ◽  
Yi Xiong ◽  
Taisheng Kang ◽  
Hua Zhu ◽  
Qiwen Yang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Human Health ◽  
Bacterial Communities ◽  
Shannon Index ◽  
Chemical Degradation ◽  
Indoor Environments ◽  
Operational Taxonomic Units ◽  
Formaldehyde Exposure ◽  
Recommended Level

AbstractIndoor formaldehyde (CH2O) exceeding the recommended level is a severe threat to human health. Few studies have investigated its effect on indoor surface bacterial communities, affecting habitants' health. This study used 20-L glass containers to mimic the indoor environment with bacterial inputs from human oral respiration. The behavior of bacterial communities responding to CH2O varied among the different CH2O levels. The bacterial community structure significantly changed over time in the 0.054 mg·m−3 CH2O group, which varied from the 0.1 mg·m−3 and 0.25 mg·m−3 CH2O groups. The Chao1 and Shannon index significantly increased in the 0.054 mg·m−3 CH2O group at 6 week, while they remained unchanged in the 0.25 mg·m−3 CH2O group. At 12 week, the Chao1 significantly increased in the 0.25 mg·m−3 CH2O group, while it remained unchanged in the 0.054 mg·m−3 CH2O group. Only a few Operational Taxonomic Units (OTUs) significantly correlated with the CH2O concentration. CH2O-induced OTUs mainly belong to the Proteobacteria and Firmicutes. Furthermore, bacterial communities formed at 6 or 12 weeks differed significantly among different CH2O levels. Functional analysis of bacterial communities showed that inferred genes related to chemical degradation and diseases were the highest in the 0.25 mg·m−3 CH2O group at 12 weeks. The development of nematodes fed with bacteria collected at 12 weeks was applied to evaluate the bacterial community's hazards. This showed significantly impaired growth in the 0.1 mg·m−3 and 0.25 mg·m−3 CH2O groups. These findings confirmed that CH2O concentration and exposure time could affect the indoor bacterial community and formed bacterial communities with a possibly more significant hazard to human health after long-term exposure to high CH2O levels.

scholarly journals Archaea in the microbial community of the reindeer rumen in the Russian Arctic

2020 ◽  
Vol 27 ◽  
pp. 00066
Author(s):  
Larisa Ilina ◽  
Valentina Filippova ◽  
Elena Yildirim ◽  
Kasim Layshev
Keyword(s):  
Microbial Community ◽  
Methanogenic Archaea ◽  
Archaeal Community ◽  
Shannon Index ◽  
Russian Arctic ◽  
Organic Substances ◽  
Autonomous District ◽  
Spring Period ◽  
First Time ◽  
Nenets Autonomous

Archaea is the least studied group of the reindeer rumen microbiocenosis. Although the functional load performed by this group of microorganisms in the rumen is large. Methane-forming archaea play a key role in the process of anaerobic decomposition of organic substances, the formation of methane. This study for the first time analyzed the composition of the archaeal part of the microbial community of the reindeer rumen using the T-RFLP method from various regions of the Russian Arctic. As a result, it was found that according to the estimates of the number of archaea by quantitative PCR in the reindeer rumen in the winter-spring period, on average, 108 genomes/g of archaea were observed in individuals of the Yamalo-Nenets Autonomous District, and 109 genomes/in animals from the Nenets Autonomous District Archean. Thus, in the winter-spring period, a lower number of archaea in the rumen was observed in the Yamalo-Nenets Autonomous District. According to the results of the T-RFLP method, 44 to 134 phylotypes were detected in the archaeal community of the reindeer rumen, the Shannon index was 2.02–3.80. The lowest content (up to 11.10 %) of methanogenic archaea of the Methanomicrobia class (including the families Methanosarcinaceae and Methanocorpusculaceae) was revealed in the Nenets Autonomous District, while their presence in individuals of the Yamalo-Nenets Autonomous District reached 36.33 %. Interestingly, in adults of the Yamalo-Nenets and Nenets Autonomous Districts, a significant decrease in the representation of methanogenic archaea of the Methanomicrobia class was noted by 1.38 (P <0.05) and 2.70 times (P <0.01), respectively, compared with young individuals (up to 2 years).

scholarly journals Disturbance During Biofilm Community Succession Promotes Cooperation and Diversity

2018 ◽  
Author(s):  
James P. Stratford ◽  
Douglas M. Hodgson ◽  
Nelli J. Beecroft ◽  
Ann Smith ◽  
Julian R. Marchesi ◽  
...  
Keyword(s):  
Time Course ◽  
Explanatory Power ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Widespread Application ◽  
Operational Taxonomic Units ◽  
Microbial Biofilms ◽  
Macro Scale ◽  
First Time ◽  
High Diversity

AbstractDiversity-disturbance relationships have found widespread application in ecology, conservation and biodiversity management. In spite of their explanatory power, these conceptual frameworks have yet to be systematically applied to understanding succession in diverse microbial biofilms. Here we investigate community assembly in biofilms formed in replicate microbial bioelectrochemical systems using time-course sequencing of community 16S rRNA genes, corresponding to hundreds of operational taxonomic units (OTUs). For the first time we present a statistical model showing that a simple diversity-disturbance relationship can be used to explain dynamic changes in high diversity biofilm communities. This simple model reveals that succession in these systems is guided towards either a low diversity, generalist-dominated biofilm or a high diversity, cooperative-specialist biofilm, depending on the level of endogenous disturbance measured within the community. The pattern observed shows remarkable symmetry with findings from macro-scale communities such as grasslands, forests and coral reefs.

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