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Map of Antarctica's western peninsula, showing the geographic locations from which the metagenomic samples were derived.
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The impacts of climate change in polar regions, like Antarctica, have the potential to alter numerous ecosystems and biogeochemical cycles. Increasing temperature and freshwater runoff from melting ice can have profound impacts on the cycling of organic and inorganic nutrients between the pelagic and benthic ecosystems.
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... in benthic sediments. In 12 of the 13 western Antarctica (WA) sites spanning from the Ross Sea to the Amundsen Sea ( Fig. 1 and 2A), we detected genes for ammonia oxidation (amoABC), the first step of the conversion of ammonia to nitrite (5). The identified amo genes were derived from Nitrosomonas and Nitrosospira (Table S1). ...
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... sediment. The genetic potential for organotrophy was also found in Antarctic sediments. Previous research suggested phytodetritus to be a large component of organic matter delivered to benthic sediments in coastal Antarctica (15). Indeed, we observe DNA sequences derived from cyanobacteria and eukaryotes, which we interpret as detrital factions (Fig. S1). All sites had comparable abundances of cyanobacterial contigs, with the exception of WA.009, which is consistent with the fact that this site had the lowest measured amount of total organic carbon (Table S1). Along with the presence of possible exogenous sources of carbon, we observed many genes coding for sugar transporters (Fig. ...
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... from the top of the cores (approximately the top 3 cm) was aseptically transferred with a spatula into conical tubes and immediately frozen (280°C). Samples were shipped frozen from the field after collection to the lab at Central Michigan University (CMU). The sampling locations, which include the Amundsen Sea, Bellingshausen Sea, and Ross Sea (Fig. 1), have low organic matter relative to the Antarctica Peninsula (15), and as the sediments were sampled in the austral summer, they were at the forefront of incoming carbon flux from the surface waters. A detailed account of sampling locations and sediment nutrient data was published previously (15), and an abbreviated list can be found ...
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... in benthic sediments. In 12 of the 13 western Antarctica (WA) sites spanning from the Ross Sea to the Amundsen Sea ( Fig. 1 and 2A), we detected genes for ammonia oxidation (amoABC), the first step of the conversion of ammonia to nitrite (5). The identified amo genes were derived from Nitrosomonas and Nitrosospira (Table S1). ...
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... sediment. The genetic potential for organotrophy was also found in Antarctic sediments. Previous research suggested phytodetritus to be a large component of organic matter delivered to benthic sediments in coastal Antarctica (15). Indeed, we observe DNA sequences derived from cyanobacteria and eukaryotes, which we interpret as detrital factions (Fig. S1). All sites had comparable abundances of cyanobacterial contigs, with the exception of WA.009, which is consistent with the fact that this site had the lowest measured amount of total organic carbon (Table S1). Along with the presence of possible exogenous sources of carbon, we observed many genes coding for sugar transporters (Fig. ...
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... from the top of the cores (approximately the top 3 cm) was aseptically transferred with a spatula into conical tubes and immediately frozen (280°C). Samples were shipped frozen from the field after collection to the lab at Central Michigan University (CMU). The sampling locations, which include the Amundsen Sea, Bellingshausen Sea, and Ross Sea (Fig. 1), have low organic matter relative to the Antarctica Peninsula (15), and as the sediments were sampled in the austral summer, they were at the forefront of incoming carbon flux from the surface waters. A detailed account of sampling locations and sediment nutrient data was published previously (15), and an abbreviated list can be found ...
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Hydrothermalism in coastal sediments strongly impacts biogeochemical processes and supports chemoautotrophy. Yet, the effect of fluid flow on microbial community composition and rates of chemoautotrophic production is unknown because rate measurements under natural conditions are difficult, impeding an assessment of the importance of these systems....
Although microbial genome sequences are relatively easily determined, assigning gene function remains a bottleneck. Consequently, relatively few genes are well characterized, leaving the function of many as either hypothetical or entirely unknown.
Citations
... Thus, high functional potentials of sulphate reduction and C degradation could result in a high accumulation of sulphide in the nativevegetated coastal sediments. Most of sulphide produced from sulphate reduction may be oxidized by chemoautotrophic S oxidizers, which could couple S oxidation with C fixation and nitrate/nitrite reduction (Garber et al., 2021;Vasquez-Cardenas et al., 2020). As microbial pathways associated with S oxidation were speculated to be a key process that detoxifies sulphide and provides energy for plant growth, the high functional potential of S oxidation in the nativevegetated coastal sediment microbiome might increase their plant primary productivity and remove toxic sulphide from plants (Rolando et al., 2022). ...
Coastal blue carbon (C) ecosystems are recognized as efficient natural C sinks and play key roles in mitigating global climate change. Microbially driven C, nitrogen (N) and sulphur (S) cycles are crucial for ecosystem functioning, but how microorganisms drive C sink formation and C sequestration in coastal sediments remains unclear.
In this study, we conducted a comprehensive analysis of amino sugars, C, N and S cycling genes/pathways and their associated taxa in coastal sediments of native (Cyperus malaccensis and Kandelia obovata) and alien (Spartina alterniflora and Sonneratia apetala) vegetation.
Compared to the alien‐vegetated coastal sediment, the native‐vegetated coastal sediment had significantly (p < 0.05) higher microbial necromass C and higher functional potentials of chemoautotrophic C fixation, C degradation, methane cycling, N2 fixation, S oxidation and sulphate reduction. Also, our analysis of coastal sediment microbiomes showed that S oxidation could be coupled with C fixation and/or nitrate/nitrite reduction. S oxidation, C degradation and C fixation were found to be key functional pathways for predicting sediment microbial necromass C. Additionally, the sulphur‐oxidizing Burkholderiales metagenome‐assembled genomes (MAGs) were a key functional group that dominated chemoautotrophic C fixation in coastal sediments.
These results suggested that chemoautotrophic S oxidizers, in particular Burkholderiales with a novel lineage, might be the key microbial group that dominates microbial necromass C formation in coastal sediments through microbial anabolism (C fixation);the coupling of microbially driven C, N and S cycling processes; and the deposition of microbially derived C. This study provides novel insights into the importance of chemoautotrophic S oxidizers for microbial necromass formation and shed new light on the microbial mechanism of C sink formation in coastal ecosystems, which also has important implications for enhancing C sequestration in coastal wetlands.
Read the free Plain Language Summary for this article on the Journal blog.
... Conversely, few metagenomic and metatranscriptomic surveys focused on climate change in Antarctica are available [56][57][58][59]. Among the relevant studies, Alarcón-Schumacher et al. [60] used metatranscriptomics and metagenomics to compare the variation in the viral and microbial active communities from a diatom-dominated phytoplankton bloom in South Shetlands. ...
The Antarctic continent is undergoing a rapid warming,
affecting microbial communities throughout its ecosystems.
This continent is a natural laboratory for studying the effect of
climate change, however, assessing the microbial communities’
responses to environmental changes is challenging from a
methodological point of view. We suggest novel experimental
designs, including multivariable assessments that apply
multiomics methods in combination with continuous
environmental data recording and new warming simulation
systems. Moreover, we propose that climate change studies in
Antarctica should consider three main objectives, including
descriptive studies, short-term temporary adaptation studies,
and long-term adaptive evolution studies. This will help us to
understand and manage the effects of climate change on the
Earth.
Download Link: https://authors.elsevier.com/c/1gp063PtAV5BdX
... Further processing from these samples involves pooling of the sediment samples from each sampling site followed by the metagenomic DNA extraction. Besides several studies have sampled sediments from 0 to 30 cm in depth to encompass total microbial diversity and their functions ( (Sadaiappan et al. 2019;Zhao et al. 2020;Garber et al. 2021) Shotgun metagenome sequencing of the DNA extracted from the sediment samples generated 1.82 million reads, yielding around 7.9 Gb bases with an average quality score and sequence length of 10.2 and 4.5 kb, respectively (Table S1). ...
Microbial carbohydrate-active enzymes (CAZyme) can be harnessed for valorization of Lignocellulosic biomass (LCB) to value-added chemicals/products. The two Indian Rivers Ganges and the Yamuna having different origins and flow, face accumulation of carbon-rich substrates due to the discharge of wastewater from adjoining paper and pulp industries, which could potentially contribute to the natural enrichment of LCB utilizing genes, especially at their confluence. We analyzed CAZyme diversity in metagenomic datasets across the sacred confluence of the Rivers Ganges and Yamuna. Functional annotation using CAZyme database identified a total of 77,815 putative genes with functional domains involved in the catalysis of carbohydrate degradation or synthesis of glycosidic bonds. The metagenomic analysis detected ~ 41% CAZymes catalyzing the hydrolysis of lignocellulosic biomass polymers- cellulose, hemicellulose, lignin, and pectin. The Beta diversity analysis suggested higher CAZyme diversity at downstream region of the river confluence, which could be useful niche for culture-based studies. Taxonomic origin for CAZymes revealed the predominance of bacteria (97%), followed by archaea (1.67%), Eukaryota (0.63%), and viruses (0.7%). Metagenome guided CAZyme diversity of the microflora spanning across the confluence of Ganges-Yamuna River, could be harnessed for biomass and bioenergy applications.
Supplementary information:
The online version contains supplementary material available at 10.1007/s13205-022-03190-7.
Sulfur (S) is an essential biological element, and S cycling is mainly driven by metabolically versatile microorganisms. The river–wetland–ocean (RWO) continuum here is defined as the dynamically connected region with estuary, wetland, and near-marine ecosystems, and it is considered a hotspot of biogeochemical cycling, especially a major biotope for S cycling. Various forms and oxidation states of S compounds are considered ideal electron donors or acceptors and are widely utilized by microorganisms via inorganic or organic S-cycling processes. The S-cycling pathways are intimately linked to the carbon (C), nitrogen, phosphorus, and metal cycles, playing crucial roles in biogeochemical cycling, C sequestration, and greenhouse gas emissions through various mechanisms in the RWO continuum. This review provides a comprehensive understanding of microbially driven S cycling in the RWO continuum. We first illustrate the importance of S cycling in this continuum, including key microorganisms and functional processes (e.g., dissimilatory sulfate reduction, S oxidation, dimethylsulfoniopropionate production, and catabolism) as well as their corresponding S flux characteristics. In particular, we emphasize recent advances in the coupling mechanisms of the S cycle with other major element cycles. We further propose important perspectives for developing microbiome engineering of S-cycling microbial communities via integration of current knowledge about the multidimensional diversity, cultivation, evolution, and interaction of S-cycling microorganisms and their coupling mechanisms in the RWO continuum, providing a new window on applying microbiome-based biotechnologies to overcome global climate challenges.
Various fields have been identified in the “omics” era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase in discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide meaningful information on the diversity and functions of microorganisms on the Earth. Therefore, the results of metagenomic studies have enabled new microbe-based applications in human health, agriculture, and the food industry, among others. This review summarizes the fundamental procedures on recent advances in bioinformatic tools. It also explores up-to-date applications of metagenomics in human health, food study, plant research, environmental sciences, and other fields. Finally, metagenomics is a powerful tool for studying the microbial world, and it still has numerous applications that are currently hidden and awaiting discovery. Therefore, this review also discusses the future perspectives of metagenomics.
A Gram-stain-negative, heterotrophic, aerobic, non-motile, rod-shaped bacterial strain (GW1-59T) belonging to the genus Lysobacter was isolated from coastal sediment collected from the Chinese Great Wall Station, Antarctica. The strain was identified using a polyphasic taxonomic approach. The strain grew well on Reasoner's 2A media and could grow in the presence of 0-4 % (w/v) NaCl (optimum, 1 %), at pH 9.0-11.0 and at 15-37 °C (optimum, 30 °C). Strain GW1-59T possessed ubiquinone-8 as the sole respiratory quinone. The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1 ω9c), iso-C15 : 0, iso-C16 : 0, iso-C17 : 0, C16 : 0 and iso-C11 : 0 3-OH. DNA-DNA relatedness with Lysobacter concretionis Ko07T, the nearest phylogenetic relative (98.5 % 16S rRNA gene sequence similarity) was 23.4 % (21.1-25.9 %). The average nucleotide identity value between strain GW1-59T and L. concretionis Ko07T was 80.1 %. The physiological and biochemical results and low level of DNA-DNA relatedness suggested the phenotypic and genotypic differentiation of strain GW1-59T from other Lysobacter species. On the basis of phenotypic, phylogenetic and genotypic data, a novel species, Lysobacter antarcticus sp. nov., is proposed. The type strain is GW1-59T (=CCTCC AB 2019390T=KCTC 72831T).
