scholarly journals Vegetation-Associated Impacts on Arctic Tundra Bacterial and Microeukaryotic Communities

2014 ◽  
Vol 81 (2) ◽  
pp. 492-501 ◽  
Author(s):  
Yu Shi ◽  
Xingjia Xiang ◽  
Congcong Shen ◽  
Haiyan Chu ◽  
Josh D. Neufeld ◽  
...  

ABSTRACTThe Arctic is experiencing rapid vegetation changes, such as shrub and tree line expansion, due to climate warming, as well as increased wetland variability due to hydrological changes associated with permafrost thawing. These changes are of global concern because changes in vegetation may increase tundra soil biogeochemical processes that would significantly enhance atmospheric CO2concentrations. Predicting the latter will at least partly depend on knowing the structure, functional activities, and distributions of soil microbes among the vegetation types across Arctic landscapes. Here we investigated the bacterial and microeukaryotic community structures in soils from the four principal low Arctic tundra vegetation types: wet sedge, birch hummock, tall birch, and dry heath. Sequencing of rRNA gene fragments indicated that the wet sedge and tall birch communities differed significantly from each other and from those associated with the other two dominant vegetation types. Distinct microbial communities were associated with soil pH, ammonium concentration, carbon/nitrogen (C/N) ratio, and moisture content. In soils with similar moisture contents and pHs (excluding wet sedge), bacterial, fungal, and total eukaryotic communities were correlated with the ammonium concentration, dissolved organic nitrogen (DON) content, and C/N ratio. Operational taxonomic unit (OTU) richness, Faith's phylogenetic diversity, and the Shannon species-level index (H′) were generally lower in the tall birch soil than in soil from the other vegetation types, with pH being strongly correlated with bacterial richness and Faith's phylogenetic diversity. Together, these results suggest that Arctic soil feedback responses to climate change will be vegetation specific not just because of distinctive substrates and environmental characteristics but also, potentially, because of inherent differences in microbial community structure.

2011 ◽  
Vol 77 (8) ◽  
pp. 2563-2572 ◽  
Author(s):  
Christopher J. Schulz ◽  
Gary W. Childers

ABSTRACTBacteroidalesare attractive as water quality indicators because of their potential to discern sources of fecal pollution, and it is presumed that these bacteria do not multiply outside their host organisms. The persistence of a fecalBacteroidalesmarker was monitored over 14 days in river water microcosms that varied in temperature from 10°C to 30°C and salinity from 0‰ to 30‰ by quantitative PCR (qPCR). Decay rates were estimated and compared to the results of other studies examining the survival and persistence ofBacteroidalesmarkers by converting decay rates from other studies to a common decay rate unit. The log-linear decay rates estimated in this work ranged from −0.18 to −1.31 ln(CT/C0) day−1, whereCTis the threshold cycle andC0is the concentration of cells at time zero, which is comparable to findings in previous studies. Salinity had a positive effect onBacteroidalesmarker persistence, while decay was more rapid at higher temperatures. Comparison of 16S rRNA gene clone libraries generated from microcosm samples indicated that most of the operational taxonomic unit (OTU) and phylogenetic diversity was found within samples and not between samples, indicating at least qualitatively that diverse lineages persist and likely have similar survival characteristics under most of the conditions examined. It was noted that the samples at higher salinities also had the smallest amount of diversity between samples as well as the lowest decay rates. This research also highlights the need for a repository of raw survival and persistence data if more sophisticated models of decay are to be employed and compared between different studies.


2004 ◽  
Vol 54 (5) ◽  
pp. 1765-1771 ◽  
Author(s):  
Stefanie Van Trappen ◽  
Tjhing-Lok Tan ◽  
Jifang Yang ◽  
Joris Mergaert ◽  
Jean Swings

Four strains of cold-adapted, strictly aerobic and facultative oligotrophic bacteria were isolated from polar seas and investigated using a polyphasic taxonomic approach. Two strains (LMG 21857T and LMG 21854) derive from Arctic sea water whereas the other two strains (LMG 21855 and LMG 21858) were isolated from Antarctic sea water. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains belong to the γ-subclass of the Proteobacteria and are related to the genus Glaciecola, with 98·0–99·7 % sequence similarity to Glaciecola mesophila and 94·2–95·3 % sequence similarity to Glaciecola punicea, their nearest phylogenetic neighbours. Two strains (LMG 21855 and LMG 21858) were identified as G. mesophila, whereas DNA–DNA hybridization results and differences in phenotypic characteristics showed that the other two strains (LMG 21857T and LMG 21854) constitute a novel species within the genus Glaciecola, with a DNA G+C content of 44·0 mol%. The isolates are Gram-negative, chemoheterotrophic, motile, rod-shaped cells that are psychrotolerant and moderately halophilic. Buds can be produced on mother cells and on prosthecae. Branch formation of prosthecae occurs. Whole-cell fatty acid profiles of the isolates are very similar and include C16 : 0 and C16 : 1 ω7c as the major fatty acid components. On the basis of genotypic and phenotypic properties, a novel species of the genus Glaciecola is described, for which the name Glaciecola polaris sp. nov. is proposed, with isolate LMG 21857T (=CIP 108324T=ARK 150T) as the type strain. An emended description of the genus Glaciecola is presented.


Idäntutkimus ◽  
2021 ◽  
Vol 28 (1) ◽  
pp. 50-65
Author(s):  
Eeva Kuikka

Artikkeli tarkastelee nenetsikirjailija Anna Nerkagin pienoisromaaneja Nogo-suvun Aniko (1976) ja Valkea jäkälä (1996) sekä venäläisen elokuvaohjaaja Vladimir Tumajevin näiden teosten pohjalta ohjaamaa elokuvaa Valkea jäkälä (2014). Lähestyn teoksia kysymällä, kuinka niissä kuvataan arktista tundraa tilana ja kuinka teoksissa kuvattu perifeerinen tila esitetään suhteessa valtakeskuksiin. Artikkelin tärkeimpinä teoreettisina viitekehyksinä toimivat geokritiikki sekä jälkikolonialistinen teoria. Nerkagin teoksissa tundra näyttäytyy muusta maasta irrallisena alkuperäiskansan toimintaympäristönä, joka kytkeytyy sekä nenetsien historiaan että näiden suhteeseen ei-inhimillisen luonnon kanssa. Erityisesti Valkean jäkälän voi nähdä myös kritisoivan yhteiskunnan tapaa laiminlyödä alueen asioiden hoitoa. Tumajevin elokuva puolestaan nojaa venäläisessä kulttuurissa vallitseviin käsityksiin arktisesta tundrasta ja heijastaa myös Venäjän 2000-luvulla aktivoitunutta tarvetta profiloitua arktisena suurvaltana. Imagined Peripheries Abstract: This article focuses on Nenets author Anna Nerkagi’s short novels Aniko of the Clan Nogo (1976) and The White Moss (1996) and their film adaptation The White Moss (2014) by Russian film director Vladimir Tumaev. I approach these works by asking how they depict the Arctic tundra as a space and how they describe the relationship between this peripheral space and the power centres. The main theoretical frameworks used are geocriticism and postcolonial theory. Nerkagi’s works depict the tundra as a region that is disconnected from the rest of the country and defined by Nenets history and the relationship with non-human nature. Especially in The White Moss, the reader can also notice a social critique of the neglect of the region. Tumaev’s film, on the other hand, relies on Russian cultural conceptions of the Arctic tundra and reflects Russia’s urge to be profiled as an Arctic superpower in the 2000s.


2020 ◽  
pp. 75-99
Author(s):  
O. I. Sumina

One of the thermokarst relief forms is baidzharakh massif — the group of mounds separated by trenches formed as a result of the underground ice-wedge polygonal networks melting (Fig. 1). Study of baidzharakh vegetation took place on the northeast coast of the Taimyr Peninsula (the Pronchishcheva Bay area) and on the New Siberian Islands (the Kotelny Island) in 1973–1974 (Sumina, 1975, 1976, 1977a, b, 1979 et al.). The aim of this paper is to produce the classification of baidzharakh mound and trenches communities according to the Brown-Blanquet approach (Westhoff, Maarel, 1978) and to compare these data with the community types earlier established on domination principle (Sumina, 1975 et al.). The information obtained in the 1970s could be helpful in a comparative assessment of the thermokarst process dynamics over the past 4 decades, as well as for comparing these processes in other regions of the Arctic. Both studied areas are located in the northern part of the arctic tundra subzone. On the Taimyr Peninsula (and in particular in the Pronchishcheva Bay area) the plakor (zonal) communities belong to the ass. Salici polaris–Hylocomietum alaskani Matveyeva 1998. Our relevés of plakor tundra on the Kotelny Island demonstrate similarity with the zonal communities of the northeast coast of the Taimyr Peninsula (Table 2). Relevés of communities of thermokarst mounds were made within their boundaries, the size of ~ 30 m². In trenches sample plots of the same area had rectangular shape according to trench width. Relevés of plakor tundra were made on 5x6 m plots. There were marked: location in relief, moistening, stand physiognomy, nanorelief, the percent of open ground patches and degree of their overgrowing, total plant cover, that of vascular plants, mosses, and lichens (especially — crustose ons), and cover estimates for each species. The shape of thermokarst mounds depends on the stage of thermodenudation processes. Flat polygons about 0.5 m height with vegetation similar to the plakor tundra are formed at the beginning of ice melting (Fig. 3, a), after which the deformation of the mounds (from eroded flat polygon (Fig. 3, b) to eroded conical mound (Fig. 3, c). Such mounds of maximal height up to 5 m are located on the middle part of steep slopes, where thermodenudation is very active. The last stage of mound destruction is slightly convex mound with a lumpy surface and vegetation, typical to snowbed sites at slope foots (Fig. 3, d, and 5). Both on watersheds and on gentle slopes mounds are not completely destroyed; and on such elongated smooth-conical mounds dense meadow-like vegetation is developed (Fig. 6). On the Kotelny Island thermokarst mounds of all described shapes occur, while in the Pronchishcheva Bay area only flat polygons, eroded flat polygons, and elongated smooth-conical mounds are presented. Under the influence of thermodenudation the plakor (zonal) vegetation is being transformed that allows to consider the most of mound and trench communities as the variants of zonal association. On the base of 63 relevés, made in 14 baidzharakh massifs, 2 variants with 7 subvariants of the ass. Salici polaris–Hylocomietum alaskani Matveyeva 1998 were established, as well as 1 variant of the azonal ass. Poo arcticae– Dupontietum fisheri Matveyeva 1994, which combines the vegetation of wet trenches with dense herbmoss cover. A detailed description of each subvariant is done. All these syntaxa are compared with the types of mound and trenh communities established previously by the domination principle (Sumina, 1975, 1976, 1979 et al.) and with Brown-Blanquet’ syntaxa published by other authors. The Brown-Blanquet approach in compare with domination principle, clearly demonstrates the similarity between zonal and baidzharakh massifs vegetation. Diagnostic species of syntaxa of baidzharakh vegetation by other authors (Matveyeva, 1994; Zanokha, 1995; Kholod, 2007, 2014; Telyatnikov et al., 2017) differ from ours. On the one hand, this is due to the fact that all mentioned researchers worked in another areas, and on the other, with different hierarchial levels of syntaxa, which are subassociations (or vicariants) in cited works or variants and subvariants in the our. Communities of mounds as well as of trenches in different regions have unlike species composition, but similar apearance, which depends on the similarity of the life form composition and community pattern, stage of their transformation and environmental factors. This fact is a base to group communities by physiognomy in order to have an opportunity of comparative analysis of baidzharakh vegetation diversity in different regions of the Arctic. In total, 6 such groups for thermokarst mounds and trenches are proposed: “tundra-like” ― vegetation of flat polygonal mounds (or trenches) is similar to the plakor (zonal) communities; “eroded tundra-like” ― tundra-like vegetation is presented as fragments, open ground occupies the main part of flat polygonal mounds; “eroded mounds with nonassociated vegetation” ― eroded mounds of various shapes up to sharp conical with absent vegetation at the top and slopes, sparse pioneer vascular plants on a bare substrate and crustose lichens and chionophilous grasses at foots; “meadow-like” ― herb stands with a participation of tundra dwarf-shrubs, mosses, and lichens on elongated smooth-conical mounds and in moderately moist trenches; “communities in snowbeds” ― thin plant cover formed by small mosses, liverworts, crustose lichens, and sparse vascular plants in snowbed habitats on destroyed slightly convex mounds with a lumpy surface and in trenches; “communities of cotton grass” or others, depending on the dominant species ― in wet trenches where vegetation is similar to the arctic hypnum bogs with dominant hygrophyte graminoids as Eriophorum scheuchzeri, E. polystachion, Dupontia fischeri et al. This sheme according to physiognomic features of thermokarst mound and trench communities, as a simplier way to assess the current dynamic stage of the baidzharakh massifs, may be useful for monitoring the thermodenudation activity in different areas of the Arctic, particularly in connection with observed climate changes (ACIA, 2004) and a possible dramatic “cascade of their environmental consequences” (Fraser et al., 2018).


The Holocene ◽  
2020 ◽  
Vol 30 (7) ◽  
pp. 1091-1096 ◽  
Author(s):  
Eleanor MB Pereboom ◽  
Richard S Vachula ◽  
Yongsong Huang ◽  
James Russell

Wildfires in the Arctic tundra have become increasingly frequent in recent years and have important implications for tundra ecosystems and for the global carbon cycle. Lake sediment–based records are the primary means of understanding the climatic influences on tundra fires. Sedimentary charcoal has been used to infer climate-driven changes in tundra fire frequency but thus far cannot differentiate characteristics of the vegetation burnt during fire events. In forested ecosystems, charcoal morphologies have been used to distinguish changes in fuel type consumed by wildfires of the past; however, no such approach has been developed for tundra ecosystems. We show experimentally that charcoal morphologies can be used to differentiate graminoid (mean = 6.77; standard deviation (SD) = 0.23) and shrub (mean = 2.42; SD = 1.86) biomass burnt in tundra fire records. This study is a first step needed to construct more nuanced tundra wildfire histories and to understand how wildfire will impact the region as vegetation and fire change in the future.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lampet Wongsaroj ◽  
Ratmanee Chanabun ◽  
Naruemon Tunsakul ◽  
Pinidphon Prombutara ◽  
Somsak Panha ◽  
...  

AbstractNortheastern Thailand relies on agriculture as a major economic activity, and has used high levels of agrochemicals due to low facility, and salty sandy soil. To support soil recovery and sustainable agriculture, local farmers have used organic fertilizers from farmed animal feces. However, knowledge about these animal fecal manures remains minimal restricting their optimal use. Specifically, while bacteria are important for soil and plant growth, an abundance and a diversity of bacterial composition in these animal fecal manures have not been reported to allow selection and adjustment for a more effective organic fertilizer. This study thereby utilized metagenomics combined with 16S rRNA gene quantitative PCR (qPCR) and sequencing to analyze quantitative microbiota profiles in association with nutrients (N, P, K), organic matters, and the other physiochemical properties, of the commonly used earthworm manure and other manures from livestock animals (including breed and feeding diet variations) in the region. Unlike the other manures, the earthworm manure demonstrated more favorable nutrient profiles and physiochemical properties for forming fertile soil. Despite low total microbial biomass, the microbiota were enriched with maximal OTUs and Chao richness, and no plant pathogenic bacteria were found based on the VFDB database. The microbial metabolic potentials supported functions to promote crop growth, such as C, N and P cyclings, xenobiotic degradation, and synthesis of bioactive compounds. Pearson’s correlation analyses indicated that the quantitative microbiota of the earthworm manure were clustered in the same direction as N, and conductivity, salinity, and water content were essential to control the microbiota of animal manures.


2009 ◽  
Vol 75 (12) ◽  
pp. 4139-4148 ◽  
Author(s):  
James P. Davis ◽  
Noha H. Youssef ◽  
Mostafa S. Elshahed

ABSTRACT We used a combination of 16S rRNA gene clone library surveys, quantitative PCR (qPCR) analysis, and fluorescent in situ hybridization to investigate the diversity, abundance, and distribution of members of candidate division SR1 in multiple habitats. Using SR1-specific 16S rRNA gene primers, we identified multiple novel SR1 lineages in four different anaerobic environments: sediments from Zodletone Spring, a sulfide- and sulfur-rich spring in southwestern Oklahoma; inner layers of microbial mats obtained from Sperm Pool, a high-temperature, low-pH pool (55°C, pH 2.5) in Yellowstone National Park; fresh bovine ruminal contents; and anaerobic freshwater pond sediments (Duck Pond) in Norman, Oklahoma. qPCR analysis indicated that SR1 members constitute a small fraction (<0.01%) of the microbial communities in Duck Pond and ruminal samples but constitute a significant fraction (11.6 and 48.7%) of the total number of bacterial 16S rRNA genes in Zodletone Spring and the inner layers of Sperm Pool microbial mat samples, respectively. By using SR1-specific fluorescent probes, filamentous cells were identified as the sole SR1 morphotype in all environments examined, with the exception of Sperm Pool, where a second bacillus morphotype was also identified. Using a full-cycle 16S rRNA approach, we show that each of these two morphotypes corresponds to a specific phylogenetic lineage identified in the Sperm Pool clone library. This work greatly expands the intralineage phylogenetic diversity within candidate division SR1 and provides valuable quantification and visualization tools that could be used for investigating the ecological roles, dynamics, and genomics of this as-yet-uncultured bacterial phylum.


2008 ◽  
Vol 74 (13) ◽  
pp. 3969-3976 ◽  
Author(s):  
Jingrang Lu ◽  
Jorge W. Santo Domingo ◽  
Regina Lamendella ◽  
Thomas Edge ◽  
Stephen Hill

ABSTRACT In spite of increasing public health concerns about the potential risks associated with swimming in waters contaminated with waterfowl feces, little is known about the composition of the gut microbial community of aquatic birds. To address this, a gull 16S rRNA gene clone library was developed and analyzed to determine the identities of fecal bacteria. Analysis of 282 16S rRNA gene clones demonstrated that the gull gut bacterial community is mostly composed of populations closely related to Bacilli (37%), Clostridia (17%), Gammaproteobacteria (11%), and Bacteriodetes (1%). Interestingly, a considerable number of sequences (i.e., 26%) were closely related to Catellicoccus marimammalium, a gram-positive, catalase-negative bacterium. To determine the occurrence of C. marimammalium in waterfowl, species-specific 16S rRNA gene PCR and real-time assays were developed and used to test fecal DNA extracts from different bird (n = 13) and mammal (n = 26) species. The results showed that both assays were specific to gull fecal DNA and that C. marimammalium was present in gull fecal samples collected from the five locations in North America (California, Georgia, Ohio, Wisconsin, and Toronto, Canada) tested. Additionally, 48 DNA extracts from waters collected from six sites in southern California, Great Lakes in Michigan, Lake Erie in Ohio, and Lake Ontario in Canada presumed to be impacted with gull feces were positive by the C. marimammalium assay. Due to the widespread presence of this species in gulls and environmental waters contaminated with gull feces, targeting this bacterial species might be useful for detecting gull fecal contamination in waterfowl-impacted waters.


2021 ◽  
Vol 9 (8) ◽  
pp. 1649
Author(s):  
Véronica L. Roman ◽  
Christophe Merlin ◽  
Marko P. J. Virta ◽  
Xavier Bellanger

EpicPCR (Emulsion, Paired Isolation and Concatenation PCR) is a recent single-cell genomic method based on a fusion-PCR allowing us to link a functional sequence of interest to a 16S rRNA gene fragment and use the mass sequencing of the resulting amplicons for taxonomic assignment of the functional sequence-carrying bacteria. Although it is interesting because it presents the highest efficiency for assigning a bacterial host to a marker, epicPCR remains a complex multistage procedure with technical difficulties that may easily impair the approach depth and quality. Here, we described how to adapt epicPCR to new gene targets and environmental matrices while identifying the natural host range of SXT/R391 integrative and conjugative elements in water microbial communities from the Meurthe River (France). We notably show that adding a supplementary PCR step allowed us to increase the amplicon yield and thus the number of reads obtained after sequencing. A comparison of operational taxonomic unit (OTU) identification approaches when using biological and technical replicates demonstrated that, although OTUs can be validated when obtained from three out of three technical replicates, up to now, results obtained from two or three biological replicates give a similar and even a better confidence level in OTU identification, while allowing us to detect poorly represented SXT/R391 hosts in microbial communities.


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