scholarly journals Bacterial, phytoplankton, and viral dynamics of meromictic Lake Cadagno offer insights into the Proterozoic ocean microbial loop

2021 ◽  
Author(s):  
Jaspreet Singh Saini ◽  
Christel Hassler ◽  
Rachel N Cable ◽  
Marion Fourquez ◽  
Francesco Danza ◽  
...  
Keyword(s):  
Meromictic Lake ◽  
Close Relative ◽  
Rrna Gene ◽  
Viral Dynamics ◽  
Comprehensive Understanding ◽  
Sulfur Bacteria ◽  
Eukaryotic Phytoplankton ◽  
Simultaneous Study ◽  
New Perspective ◽  
Secondary Productivity

Meromictic Lake Cadagno, with its permanent stratification and persistent microbial bloom within the anoxic chemocline, serves as an ancient ocean analogue. Although the lake has been studied for over 25 years, the absence of simultaneous study of the bacteria, phytoplankton, and viruses, together with primary and secondary productivity, has hindered a comprehensive understanding of its microbial food web. This study evaluated the identities, abundances, and productivity of microbes in the context of nutrient biogeochemical cycling across the stratified depths of Lake Cadagno. Photosynthetic pigments and chloroplast 16S rRNA gene phylogenies suggested high abundances of eukaryotic phytoplankton, primarily Chlorophyta, through the water column. Of these, a close relative of Ankyra judayi, a high-alpine adapted chlorophyte, peaked with oxygen in the mixolimnion, while Closteriopsis-related chlorophytes peaked in the chemocline and monimolimnion. Chromatium, a genus of anoxygenic phototrophic sulfur bacteria, dominated the chemocline along with Lentimicrobium, a genus of known fermenters whose abundance was newly reported in Lake Cadagno. Secondary production peaked in the chemocline, suggesting anoxygenic primary producers depended on heterotrophic nutrient remineralization. Virus-to-microbe ratios (VMR) peaked in the zone of high phytoplankton abundances, yet were at a minimum at the peak of Chromatium, dynamic trends that suggest viruses may play a role in the modulation of oxygenic and anoxygenic photo- and chemosynthesis in Lake Cadagno. Through the combined analysis of bacterial, eukaryotic, viral, and biogeochemical dynamics of Lake Cadagno, this study provides a new perspective on the biological and geochemical connections that comprised the food webs of the Proterozoic ocean.

scholarly journals Thiocystis chemoclinalis sp. nov. and Thiocystis cadagnonensis sp. nov., motile purple sulfur bacteria isolated from the chemocline of a meromictic lake

2011 ◽  
Vol 61 (7) ◽  
pp. 1682-1687 ◽  
Author(s):  
Sandro Peduzzi ◽  
Allana Welsh ◽  
Antonella Demarta ◽  
Paola Decristophoris ◽  
Raffaele Peduzzi ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Phylogenetic Analyses ◽  
Distinct Species ◽  
Meromictic Lake ◽  
Purple Sulfur Bacteria ◽  
Rrna Gene ◽  
Bacterial Populations ◽  
Sulfur Bacteria ◽  
Type Strains ◽  
Sequence Similarities

Two isolates, designated CadH11T and Cad448T, representing uncultured purple sulfur bacterial populations H and 448, respectively, in the chemocline of Lake Cadagno, a crenogenic meromictic lake in Switzerland, were obtained using enrichment and isolation conditions that resembled those used for cultured members of the genus Thiocystis. Phenotypic, genotypic and phylogenetic analyses of these isolates confirmed their assignment to the genus Thiocystis. However, 16S rRNA gene sequence similarities of 98.2 % between CadH11T and Cad448T, and similarities of 97.7 and 98.5 %, respectively, with their closest cultured relative Thiocystis gelatinosa DSM 215T, as well as differences in DNA G+C content and carbon source utilization suggested that the isolates belonged to two distinct species. DNA–DNA hybridization of CadH11T and Cad448T with T. gelatinosa DSM 215T showed relatedness values of 46.4 and 60.8 %, respectively; the relatedness value between CadH11T and Cad448T was 59.2 %. Based on this evidence, strains CadH11T and Cad448T represent two novel species within the genus Thiocystis, for which the names Thiocystis chemoclinalis sp. nov. and Thiocystis cadagnonensis sp. nov. are proposed, respectively. The type strains of T. chemoclinalis sp. nov. and T. cadagnonensis sp. nov. are CadH11T ( = JCM 15112T  = KCTC 5954T) and Cad448T ( = JCM 15111T  = KCTC 15001T), respectively.

scholarly journals In Situ Analysis of Sulfate-Reducing Bacteria Related to Desulfocapsa thiozymogenes in the Chemocline of Meromictic Lake Cadagno (Switzerland)

2000 ◽  
Vol 66 (2) ◽  
pp. 820-824 ◽  
Author(s):  
Mauro Tonolla ◽  
Antonella Demarta ◽  
Sandro Peduzzi ◽  
Dittmar Hahn ◽  
Raffaele Peduzzi
Keyword(s):  
Sulfate Reducing Bacteria ◽  
Comparative Sequence Analysis ◽  
Potential Interaction ◽  
Meromictic Lake ◽  
Rrna Gene ◽  
Sulfate Reducing ◽  
Sulfur Bacteria ◽  
The Family ◽  
Reducing Bacteria

ABSTRACT Comparative sequence analysis of a 16S rRNA gene clone library from the chemocline of the meromictic Lake Cadagno (Switzerland) retrieved two clusters of sequences resembling sulfate-reducing bacteria within the family Desulfovibrionaceae. In situ hybridization showed that, similar to sulfate-reducing bacteria of the familyDesulfobacteriaceae, bacteria of one cluster with similarity values to the closest cultured relatives of between 92.6 and 93.1% resembled free cells or cells loosely attached to other cells or debris. Bacteria of the second cluster closely related toDesulfocapsa thiozymogenes DSM7269 with similarity values between 97.9 and 98.4% were generally associated with aggregates of different small-celled phototrophic sulfur bacteria, suggesting a potential interaction between the two groups of bacteria.

In Situ Analysis of Phototrophic Sulfur Bacteria in the Chemocline of Meromictic Lake Cadagno (Switzerland)

1999 ◽  
Vol 65 (3) ◽  
pp. 1325-1330 ◽  
Author(s):  
Mauro Tonolla ◽  
Antonella Demarta ◽  
Raffaele Peduzzi ◽  
Dittmar Hahn
Keyword(s):  
Comparative Sequence Analysis ◽  
Meromictic Lake ◽  
Gene Clone ◽  
Rrna Gene ◽  
Oligonucleotide Probes ◽  
Phototrophic Sulfur Bacteria ◽  
Sulfur Bacteria ◽  
Tight Cluster ◽  
Type Strains

ABSTRACT Comparative sequence analysis of a 16S rRNA gene clone library from the chemocline of the meromictic Lake Cadagno (Switzerland) revealed the presence of a diverse number of phototrophic sulfur bacteria. Sequences resembled those of rRNA of type strains Chromatium okenii DSM169 and Amoebobacter purpureus DSM4197, as well as those of four bacteria forming a tight cluster with A. purpureus DSM4197 and Lamprocystis roseopersicinaDSM229. In situ hybridization with fluorescent (Cy3 labeled) oligonucleotide probes indicated that all large-celled phototrophic sulfur bacteria in the chemocline of Lake Cadagno were represented byC. okenii DSM169, while small-celled phototrophic sulfur bacteria consisted of four major populations with different distribution profiles in the chemocline indicating different ecophysiological adaptations.

scholarly journals Microbial loop of a Proterozoic ocean analogue

2021 ◽  
Author(s):  
Jaspreet S Saini ◽  
Christel Hassler ◽  
Rachel Cable ◽  
Marion Fourquez ◽  
Francesco Danza ◽  
...  
Keyword(s):  
Organic Matter ◽  
Secondary Production ◽  
Microbial Loop ◽  
Biological Data ◽  
Rrna Gene ◽  
Data Types ◽  
Sulfur Bacteria ◽  
Eukaryotic Phytoplankton ◽  
Essential Components ◽  
Parachlorella Kessleri

AbstractMeromictic Lake Cadagno, an ancient ocean analogue, is known for its permanent stratification and persistent anoxygenic microbial bloom within the chemocline. Although the anaerobic microbial ecology of the lake has been extensively studied for at least 25 years, a comprehensive picture of the microbial food web linking the bacterial layer to phytoplankton and viruses, with explicit measures of primary and secondary production, is still missing. This study sought to understand better the abundances and productivity of microbes in the context of nutrient biogeochemical cycling across the stratified zones of Lake Cadagno. Photosynthetic pigments and chloroplast 16S rRNA gene phylogenies suggested the presence of eukaryotic phytoplankton through the water column. Evidence supported high abundances of Ankyra judayi, a high-alpine adapted chlorophyte, in the oxic mixolimnion where oxygenic-primary production peaked. Through the low- and no-oxygen chemocline and monimolimnion, chlorophytes related to Closteriopsis acicularis, a known genus of meromictic lakes, and Parachlorella kessleri were observed. Chromatium, anoxygenic phototrophic sulfur bacteria, dominated the chemocline along with Lentimicrobium, a genus of known fermenters whose abundance was newly reported in Lake Cadagno. Secondary production peaked in the chemocline suggesting primary producers depend on heterotrophs for nutrient remineralization. As previously observed, sulfur-reducing bacteria (SRBs), especially Desulfocapsa and Desulfobulbus, were present in the chemocline and anoxic monimolimnion. Virus-to-microbe ratios (VMR) peaked in the zone of phytoplankton yet were at a minimum at the peak of Chromatium. These dynamic trends suggest viruses may play a role in the modulation of oxygenic and anoxygenic photo- and chemosynthesis in Lake Cadagno and other permanently stratified systems.ImportanceAs a window to the past, the study offers insights into the role of microbial guilds of Proterozoic ocean chemoclines in the production and recycling of organic matter of sulfur- and ammonia-containing ancient oceans. The new observations described here suggest that eukaryotic algae were persistent in the low oxygen upper-chemocline in association with purple and green sulfur bacteria in the lower half of the chemocline. Further, this study provides the first insights into Lake Cadagno viral ecology. High viral abundances suggested viruses may be essential components of the chemocline where their activity may result in the release and recycling of organic matter. The framework developed in this study through the integration of diverse geochemical and biological data types lays the foundation for future studies to quantitatively resolve the processes performed by discrete populations comprising the microbial loop in this early anoxic ocean analogue.

scholarly journals Anoxygenic photo- and chemosynthesis of phototrophic sulfur bacteria from an alpine meromictic lake

2021 ◽  
Author(s):  
Francesco Di Nezio ◽  
Clarisse Beney ◽  
Samuele Roman ◽  
Francesco Danza ◽  
Antoine Buetti-Dinh ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Meromictic Lake ◽  
Purple Sulfur Bacterium ◽  
Phototrophic Sulfur Bacteria ◽  
Anaerobic Microorganisms ◽  
Sulfur Bacteria ◽  
Pure Cultures ◽  
Chlorobium Phaeobacteroides ◽  
Anoxic Environment ◽  
Dark Carbon Fixation

Abstract Meromictic lakes are interesting ecosystems to study anaerobic microorganisms due their permanent stratification allowing the formation of a stable anoxic environment. The crenogenic meromictic Lake Cadagno harbors an important community of anoxygenic phototrophic sulfur bacteria responsible for almost half of its total productivity. Besides their ability to fix CO2 through photosynthesis, these microorganisms also showed high rates of dark carbon fixation via chemosyntesis. Here, we grew in pure cultures three populations of anoxygenic phototrophic sulfur bacteria previously isolated from the lake, accounting for 72.8% of the total microbial community, and exibiting different phenotypes: 1) the motile, large-celled purple sulfur bacterium (PSB) Chromatium okenii, 2) the small-celled PSB Thiodictyon syntrophicum, and 3) the green sulfur bacterium (GSB) Chlorobium phaeobacteroides. We measured their ability to fix CO2 through photo- and chemo-synthesis, both in situ in the lake and in laboratory under different incubation conditions. We also evaluated the efficiency and velocity of H2S photo-oxidation, an important reaction in the anoxygenic photosynthesis process. Our results confirm that phototrophic sulfur bacteria strongly fix CO2 in the presence of light and that oxygen increases chemosynthesis at night, in laboratory conditions. Moreover, substancial differences were displayed between the three selected populations in terms of activity and abundance.

Methanobacterium lacus sp. nov., isolated from the profundal sediment of a freshwater meromictic lake

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1625-1629 ◽  
Author(s):  
Guillaume Borrel ◽  
Keith Joblin ◽  
Annie Guedon ◽  
Jonathan Colombet ◽  
Vincent Tardy ◽  
...  
Keyword(s):  
Rumen Fluid ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Meromictic Lake ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Lake Pavin

An autotrophic, hydrogenotrophic methanogen, designated strain 17A1T, was isolated from the profundal sediment of the meromictic Lake Pavin, France. The cells of the novel strain, which were non-motile, Gram-staining-negative rods that measured 2–15 µm in length and 0.2–0.4 µm in width, grew as filaments. Strain 17A1T grew in a mineral medium and its growth was stimulated by the addition of yeast extract, vitamins, acetate or rumen fluid. Penicillin, vancomycin and kanamycin reduced growth but did not completely inhibit it. Growth occurred at 14–41 °C (optimum 30 °C), at pH 5.0–8.5 (optimum pH 6.5) and with 0–0.4 M NaCl (optimum 0.1 M). The novel strain utilized H2/CO2 and methanol/H2 as substrates but not formate, acetate, methylamine/H2, isobutanol or 2-propanol. Its genomic DNA G+C content was 37.0 mol%. In phylogenetic analyses based on 16S rRNA gene sequences, strain 17A1T appeared to be a member of the genus Methanobacterium , with Methanobacterium beijingense 8-2T (96.3 % sequence similarity) identified as the most closely related established species. Based on phenotypic and phylogenetic data, strain 17A1T represents a novel species of methanogen within the genus Methanobacterium , for which the name Methanobacterium lacus sp. nov. is proposed. The type strain is 17A1T ( = DSM 24406T = JCM 17760T).

scholarly journals Clostridium schirmacherense sp. nov., an obligately anaerobic, proteolytic, psychrophilic bacterium isolated from lake sediment of Schirmacher Oasis, Antarctica

2006 ◽  
Vol 56 (4) ◽  
pp. 715-720 ◽  
Author(s):  
Syed Imteyaz Alam ◽  
Aparna Dixit ◽  
G. S. N. Reddy ◽  
S. Dube ◽  
Meehir Palit ◽  
...  
Keyword(s):  
Cell Mass ◽  
Basal Medium ◽  
Close Relative ◽  
Rrna Gene ◽  
Psychrophilic Bacterium ◽  
Fermentation Products ◽  
Obligately Anaerobic ◽  
Schirmacher Oasis ◽  
Genome Level ◽  
Clostridium Subterminale

A novel obligately anaerobic, proteolytic bacterium, designated AP15T, was isolated from lake sediments of Schirmacher Oasis, Antarctica. The bacterium produced maximum cell mass between 5 and 10 °C in an anaerobic basal medium containing 0·5 % tryptone and peptone. The strain grew optimally at a pH around 8·0 and tolerated NaCl up to a concentration of 7·5 %. It contained diphosphatidylglycerol as the major phospholipid and C15 : 0, C16 : 0 and C17 : 0 as the major cellular fatty acids. Several amino acids, including arginine, leucine, isoleucine, cysteine, glutamate and serine, supported growth. Glutamate was degraded to acetate, propionate, CO2 and H2. In addition, the strain degraded carbohydrates including glucose, raffinose, adonitol, ribose and rhamnose. The main fermentation products during growth on glucose were H2, CO2, formate, acetate, propionate and isovalerate. The DNA G+C content of the bacterium was 24 mol%. On the basis of a phylogenetic analysis, strain AP15T is identified as a close relative of Clostridium subterminale ATCC 25774T, with which it shares 99·5 % similarity at the 16S rRNA gene sequence level; however, it exhibits a low DNA–DNA binding value (55 %) to this strain at the whole-genome level. In addition to showing other major differences with respect to C. subterminale and other members of the genus Clostridium, AP15T also exhibits phenotypic differences. On the basis of these differences, strain AP15T is identified as representing a novel species of the genus Clostridium, for which the name Clostridium schirmacherense sp. nov. is proposed. The type strain is AP15T (=DSM 17394T=JCM 13289T).

Constructing a Defined Starter for Multispecies Vinegar Fermentation via Evaluating the Vitality and Dominance of Functional Microbes in Autochthonous Starter

2021 ◽  
Author(s):  
Ting Huang ◽  
Zhen-Ming Lu ◽  
Ming-Ye Peng ◽  
Li-Juan Chai ◽  
Xiao-Juan Zhang ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Starter Culture ◽  
Titratable Acidity ◽  
Natural Food ◽  
Rrna Gene ◽  
Comprehensive Understanding ◽  
Acid Fermentation ◽  
Operational Taxonomic Units ◽  
Core Species ◽  
Efficient Fermentation

Mature vinegar culture has usually been used as a type of autochthonous starter for rapidly initiate initiating the next batch of acetic acid fermentation (AAF) and maintaining the batch-to-batch uniformity of AAF in the production of traditional cereal vinegar. However, the vitality and dominance of functional microbes in autochthonous starters remain unclear, which hinders further improvement of fermentation yield and production. Here, based on metagenomic (MG), metatranscriptomic (MT), and 16S rRNA gene sequencings, 11 bacterial operational taxonomic units (OTUs) with significant metabolic activity (MT/MG ratio >1) and dominance (relative abundance >1%) were targeted in the autochthonous vinegar starter, all of which were assigned to 4 species ( Acetobacter pasteurianus , Lactobacillus acetotolerans , L. helveticus , Acetilactobacillus jinshanensis ). Then, we evaluated the successions and interactions of these 11 bacterial OTUs at different AAF stages. Last, a defined starter was constructed with 4 core species isolated from the autochthonous starter ( A. pasteurianus , L. acetotolerans , L. helveticus , Ac. jinshanensis ). The defined starter culture could rapidly initiate the AAF in a sterile or unsterilized environment and similar dynamics of metabolites (ethanol, titratable acidity, acetic acid, lactic acid, and volatile compounds) and environmental indexes (temperature, pH) of fermentation were observed as compared with that of autochthonous starter ( P > 0.05). This work provides a method to construct a defined microbiota from a complex system while preserving its metabolic function. IMPORTANCE Complex microorganisms are beneficial to the flavor formation in natural food fermentation, but they also pose challenges to the mass production of standardized products. It is attractive to construct a defined starter to rapidly initiate fermentation process and significantly improve fermentation yield. This study provides a comprehensive understanding of vital and dominant species in the autochthonous vinegar starter via multi-omics, and designs a defined microbial community for the efficient fermentation of cereal vinegar.

Caterpillar gut and host plant phylloplane mycobiomes differ: a new perspective on fungal involvement in insect guts

2020 ◽  
Vol 96 (9) ◽  
Author(s):  
Denisa višňovská ◽  
Petr Pyszko ◽  
Martin Šigut ◽  
Martin Kostovčík ◽  
Miroslav Kolařík ◽  
...  
Keyword(s):  
Jaccard Index ◽  
Herbivorous Insects ◽  
Rrna Gene ◽  
Its2 Rdna ◽  
Leaf Sample ◽  
Dna Metabarcoding ◽  
Genus Richness ◽  
Qualitative Similarity ◽  
Feeding Substrate ◽  
New Perspective

ABSTRACT Compared with the highly diverse microbiota of leaves, herbivorous insects exhibit impoverished gut microbial communities. Research to date has focused on the bacterial component of these gut microbiomes, neglecting the fungal component. As caterpillar gut bacterial microbiomes are derived strongly from their diet, we hypothesized that their mycobiomes would reflect the host leaf mycobiomes. Using the ITS2 rDNA and V5–V6 16S rRNA gene regions for DNA metabarcoding of caterpillar gut and host leaf sample pairs we compared their mycobiome genus diversity and compositions and identified genera associated with caterpillar guts. Leaves and caterpillar guts harbored different mycobiomes with quite low qualitative similarity (Jaccard index = 38.03%). The fungal genera most significantly associated with the caterpillar gut included Penicillium, Mucor and unidentified Saccharomycetales, whereas leaf-associated genera included Holtermanniella, Gibberella (teleomorph of Fusarium) and Seimatosporium. Although caterpillar gut and leaf mycobiomes had similar genus richness overall, this indicator was not correlated for individual duplets. Moreover, as more samples entered the analysis, mycobiome richness increased more rapidly in caterpillar guts than in leaves. The results suggest that the mycobiota of the caterpillar gut differs from that of their feeding substrate; further, the mycobiomes appear to be richer than the well-studied bacterial microbiotas.

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