Seasonal variation and human impacts of the river biofilm bacterial communities in the Shiting River in southeastern China

Bacterial communities in epilithic biofilm plays an important role in biogeochemistry processes in freshwater ecosystems. Nevertheless, our understanding of the geographical and seasonal variations of the composition of bacterial communities in the biofilm of gravels on river bed is still limited. Various anthropogenic activities also influence the biofilm bacteria in gravel rivers. By taking the Shiting River in the upper Yangtze River basin in Sichuan Province as an example, we studied the geographical and seasonal variations of epilithic bacteria and the impacts of weirs and other human activities (e.g., sewage pollution). The river has experienced severe degradation since the Ms 8.0 Wenchuan Earthquake, and weirs were constructed to prevent bed erosion. We collected epilithic biofilms samples at 17 sites along ~ 30 km river reach of the Shiting River in the autumn of 2021 and the summer of 2022, respectively. We applied 16S rRNA gene high-throughput sequencing technology and Functional Annotation of Prokaryotic Taxa (FAPROTAX) to analyze the seasonal and biogeographic patterns and potential functions of the biofilm bacterial communities. The results showed that epilithic bacteria from the two surveys exhibited variation in community composition, bacterial diversity and potential functions. The bacteria samples collected in the autumn have much higher alpha diversity and richness than those collected in the summer. Bacterial richness and diversity were lower downstream of the weirs than upstream. Low diversity was observed at a sampling site influenced by sewage inflow, which contains high level of nitrogen-related chemicals.

The relationships between heavy metals and bacterial communities in a coal gangue site

Coal is the main source of energy for China's economic development, but coal gangue dumps are a major source of heavy metal pollution. Bacterial communities have a major effect on the bioremediation of heavy metals in coal gangue dumps. The effects of different concentrations of heavy metals on the composition of bacterial communities in coal gangue sites remain unclear. Soil bacterial communities from four gangue sites that vary in natural heavy metal concentrations were investigated using high-throughput sequencing in this study. Correlations among bacterial communities, heavy metal concentrations, physicochemical properties of the soil, and the composition of dissolved organic matter of soil in coal gangue dumps were also analyzed. Our results indicated that Actinobacteriota, Proteobacteria, Chloroflexi, Acidobacteriota, and Gemmatimonadota were the bacterial taxa most resistant to heavy metal stress at gangue sites. Heavy metal contamination may be the main cause of changes in bacterial communities. Heavy metal pollution can foster mutually beneficial symbioses between microbial species. Microbial-derived organic matter was the main source of soil organic matter in unvegetated mining areas, and this could affect the toxicity and transport of heavy metals in soil. Polar functional groups such as hydroxyl and ester groups (A_226-400) play an important role in the reaction of cadmium (Cd) and lead (Pb), and organic matter with low molecular weight (S_R) tends to bind more to mercury (Hg). In addition to heavy metals, the content of nitrogen (N), phosphorus (P), and total organic carbon (TOC) also affected the composition of the bacterial communities; TOC had the strongest effect, followed by N, SOM, and P. Our findings have implications for the microbial remediation of heavy metal-contaminated soils in coal gangue sites and sustainable development.

Assembly and Network Stability of Planktonic Microorganisms under the Influence of Salinity Gradient: an Arctic Case Study from the Lena River Estuary to the Laptev Sea

The diversity and primary productivity in the Arctic ecosystem are rapidly changing due to global warming. Microorganisms play a vital role in biogeochemical cycling. However, the diversity of planktonic microorganism communities in the Laptev Sea, one of the most important marginal seas of the Western Arctic Ocean, have not been studied sufficiently in depth. The diversity and community structure of the planktonic microorganisms in the surface water were investigated at 20 stations on the Lena River flowing into the Laptev Sea. Multivariate statistical analyses demonstrated clear spatial patterns in the α diversity and community structure for microorganisms under different salinity levels. Co-occurrence networks of microbial communities revealed that spatial variation promoted differentiation of the characteristics and stability of microbial networks in the Laptev Sea. Contrary to expectations, abundant taxa were found to not have a large influence on the stability and resilience of microbial interactions in the region. On the contrary, less-abundant taxa were found to have far greater influence. The stability and resilience of the prokaryotic and microeukaryotic networks in the Lena River estuary and the continental shelf provided valuable insights into the impact of freshwater and land inflow disturbances on microbial assemblage. Overall, these results enhance our understanding of the composition of microbial communities and provide insights into how spatial changes of abundant versus rare species alter the nature and stability of microbial networks from the Lena River estuary to the Laptev Sea. In addition, this study explored microbial interactions and their ability to resist future disturbances. IMPORTANCE The regime of the Laptev Sea depends closely on the runoff of the Lena River. Microorganisms are essential components of aquatic food webs and play a significant role in polar ecosystems. In this study, we provided a basic microbial data set as well as new insights into the microbial networks from the Lena River estuary to the Laptev Sea, while exploring their potential to resist future disturbances. A comprehensive and systematic study of the community structure and function of the planktonic microorganisms in the Laptev Sea would greatly enhance our understanding of how polar microbial communities respond to the salinity gradient under climate warming.

Metagenomic insights into the antibiotic resistome in freshwater and seawater from an Antarctic ice-free area

The comprehensive profiles of antibiotic resistance genes (ARGs) in the Antarctic water environments and their potential health risks are not well understood. The present study characterized the bacterial community compositions and ARG profiles of freshwater (11 samples) and seawater (28 samples) around the Fildes Region (an ice-free area in Antarctica) using a shotgun metagenomic sequencing approach for the first time. There were significant differences in the compositions of the bacterial community and ARG profiles between freshwater and seawater. In the 39 water samples, 114 ARG subtypes belonging to 15 ARG types were detectable. In freshwater, the dominant ARGs were related to multidrug and rifamycin resistance. In seawater, the dominant ARGs were related to peptide, multidrug, and beta-lactam resistance. Both the bacterial community compositions and ARG profiles were significantly related to certain physicochemical properties (e.g., pH, salinity, NO₃^-). Procrustes analysis revealed a significant correlation between the bacterial community compositions and ARG profiles of freshwater and seawater samples. A total of 31 metagenome-assembled genomes (MAGs) carrying 35 ARG subtypes were obtained and identified. The results will contribute to a better evaluation of the ARG contamination in relation to human health in the Antarctic aquatic environments.

Biogeography of Southern Ocean Active Prokaryotic Communities Over a Large Spatial Scale

The activity of marine microorganisms depends on community composition, yet, in some oceans, less is known about the environmental and ecological processes that structure their distribution. The objective of this study was to test the effect of geographical distance and environmental parameters on prokaryotic community structure in the Southern Ocean (SO). We described the total (16S rRNA gene) and the active fraction (16S rRNA-based) of surface microbial communities over a ~6,500 km longitudinal transect in the SO. We found that the community composition of the total fraction was different from the active fraction across the zones investigated. In addition, higher α-diversity and stronger species turnover were displayed in the active community compared to the total community. Oceanospirillales, Alteromonadales, Rhodobacterales, and Flavobacteriales dominated the composition of the bacterioplankton communities; however, there were marked differences at the order level. Temperature, salinity, silicic acid, particulate organic nitrogen, and particulate organic carbon correlated with the composition of bacterioplankton communities. A strong distance–decay pattern between closer and distant communities was observed. We hypothesize that it was related to the different oceanic fronts present in the Antarctic Circumpolar Current. Our findings contribute to a better understanding of the complex arrangement that shapes the structure of bacterioplankton communities in the SO.

Estuarine salinity gradient governs sedimentary bacterial community but not antibiotic resistance gene profile

Antibiotic resistance gene (ARG) pollution in estuarine environment has drawn great attention, and it is not clear if the physical and chemical parameters such as salinity, total organic carbon, total nitrogen, total phosphorus and antibiotics affects the distribution of ARGs. Herein, we deciphered the ARG profiles and microbial community compositions in sediments from Jiulong River Estuary (JRE) and Min River Estuary (MRE) of China using high-throughput sequencing-based metagenomics analysis. Furthermore, we explored the influence of salinity on bacterial community and ARG profiles. The results showed that Proteobacteria, Chloroflexi, and Acidobacteria were the dominant phyla in these two estuaries. The abundance of ARGs ranged from 1.05 × 10^-1 to 2.93 × 10^-1 copy of ARG per copy of 16S rRNA gene in all the sediment samples and the profiles of ARGs presented similar patterns in two estuaries. Multidrug resistance genes were the dominant ARG types in both estuaries, with an overall abundance of 2.39 × 10^-2-1.07 × 10^-1 copy of ARG per copy of 16S rRNA gene, followed by genes conferring resistance to bacitracin and macrolide-lincosamide-streptogramin. Salinity was an important influencing factor on the bacterial community but not on the ARG profiles. Instead, stochastic processes exerted the main influence on the distribution of ARGs. The comparison of ARG profiles among estuary sediments, marine sediments, and samples from anthropogenic pollution environments revealed remarkable similarity of ARG profiles between samples from estuary sediments and those from municipal wastewater treatment plants. These results suggested that the complex emission of anthropogenic pollution could cause the stochastic ecological pattern of ARGs.

Planktonic microbial eukaryotes in polar surface waters: recent advances in high-throughput sequencing

Marine microbial eukaryotes are important primary producers and play critical roles in key biogeochemical cycles. Recent advances in sequencing technology have focused attention on the extent of microbial biodiversity, revealing a huge, previously underestimated phylogenetic diversity with many new lineages. This technology has now become the most important tool to understand the ecological significance of this huge and novel diversity in polar oceans. In particular, high-throughput sequencing technologies have been successfully applied to enumerate and compare marine microbial diversity in polar environments. Here, a brief overview of polar microbial eukaryote diversity, as revealed by in-situ surveys of the high-throughput sequencing on 18S rRNA gene, is presented. Using these 'omic' approaches, further attention still needs to be focused on differences between specific locations and/or entire polar oceans and on bipolar comparisons of diversity and distribution.

Annual phytoplankton dynamics in coastal waters from Fildes Bay, Western Antarctic Peninsula

Year-round reports of phytoplankton dynamics in the West Antarctic Peninsula are rare and mainly limited to microscopy and/or pigment-based studies. We analyzed the phytoplankton community from coastal waters of Fildes Bay in the West Antarctic Peninsula between January 2014 and 2015 using metabarcoding of the nuclear and plastidial 18/16S rRNA gene from both size-fractionated and flow cytometry sorted samples. Overall 14 classes of photosynthetic eukaryotes were present in our samples with the following dominating: Bacillariophyta (diatoms), Pelagophyceae and Dictyochophyceae for division Ochrophyta, Mamiellophyceae and Pyramimonadophyceae for division Chlorophyta, Haptophyta and Cryptophyta. Each metabarcoding approach yielded a different image of the phytoplankton community with for example Prymnesiophyceae more prevalent in plastidial metabarcodes and Mamiellophyceae in nuclear ones. Diatoms were dominant in the larger size fractions and during summer, while Prymnesiophyceae and Cryptophyceae were dominant in colder seasons. Pelagophyceae were particularly abundant towards the end of autumn (May). In addition of Micromonas polaris and Micromonas sp. clade B3, both previously reported in Arctic waters, we detected a new Micromonas 18S rRNA sequence signature, close to, but clearly distinct from M. polaris, which potentially represents a new clade specific of the Antarctic. These results highlight the need for complementary strategies as well as the importance of year-round monitoring for a comprehensive description of phytoplankton communities in Antarctic coastal waters.

Exploring the effects of volcanic eruption disturbances on the soil microbial communities in the montane meadow steppe

Volcanic eruptions are important components of natural disturbances that provide a model to explore the effects of volcanic eruption disturbances on soil microorganisms. Despite widespread research, to the best of our knowledge, no studies of volcanic eruption disturbances have investigated the effects on soil microbial communities in the montane meadow steppe. To address this gap, we meticulously investigated the characteristics of the soil microbial communities from the volcano and steppe sites using Illumina MiSeq high-throughput sequencing. Hierarchical clustering analysis and principal coordinate analysis (PCoA) showed that the soil microbial communities from the volcano and steppe sites differed. The diversity and richness of the soil microbial communities from the steppe sites were significantly higher than at the volcano sites (P < 0.05), and the soil microbial communities in the steppe sites had higher stability. The effects of volcanic eruption disturbances on the bacterial community development are greater than its effects on the fungal communities. The environmental filtering of volcanic eruptions selectively retained some special microorganisms (i.e., Conexibacter, Agaricales, and Gaiellales) with strong adaptability to the environmental disturbances, enhanced metabolic activity for sodium and calcium reabsorption, and increased relative abundances of the lichenized saprotrophs. The soil microbial communities from the volcano and steppe sites cooperate to form complex networks of species interactions, which are strongly influenced by the interaction of the soil and vegetation factors. Our findings provide new information on the effects of volcanic eruption disturbances on the soil microbial communities in the montane meadow steppe.

Distribution and Control of Bacterial Community Composition in Marian Cove Surface Waters, King George Island, Antarctica during the Summer of 2018

Marian Cove is experiencing some of the most rapid environmental changes in the Antarctic region; however, little is known about the response of bacterial communities to these changes. The main purpose of this study was to investigate the spatial variation of physical‒biogeochemical‒bacterial community features in the Marian Cove surface waters and the environmental parameters governing the spatial variation in the bacterial community composition during the summer of 2018. The Marian Cove surface waters are largely composed of two different characteristics of water masses: relatively low-temperature, -salinity, and -nutrient surface glacier water (named SGW) and relatively high-temperature, -salinity, and -nutrient surface Maxwell Bay water (named SMBW). The SGW bacterial communities were dominated by unclassified Cryomorphaceae, Sedimenticola, and Salibacter genera, while the SMBW bacterial communities were dominated by Sulfitobacter, Arcobacter, and Odoribacter genera. Spatial variations in bacterial community composition were mainly attributed to physical and biogeochemical characteristics, suggesting that the bacterial community composition of the Marian Cove surface waters is mainly determined by environmental characteristics. These findings provide a foundation to improve the understanding of bacterial community variations in response to a rapidly changing Marian Cove in the Antarctic.

Assessing Viral Abundance and Community Composition in Four Contrasting Regions of the Southern Ocean

We explored how changes of viral abundance and community composition among four contrasting regions in the Southern Ocean relied on physicochemical and microbiological traits. During January-February 2015, we visited areas north and south of the South Orkney Islands (NSO and SSO) characterized by low temperature and salinity and high inorganic nutrient concentration, north of South Georgia Island (NSG) and west of Anvers Island (WA), which have relatively higher temperatures and lower inorganic nutrient concentrations. Surface viral abundance (VA) was highest in NSG (21.50 ± 10.70 × 10⁶ viruses mL^-1) and lowest in SSO (2.96 ± 1.48 × 10⁶ viruses mL^-1). VA was positively correlated with temperature, prokaryote abundance and prokaryotic heterotrophic production, chlorophyll a, diatoms, haptophytes, fluorescent organic matter, and isoprene concentration, and was negatively correlated with inorganic nutrients (NO_3-, SiO₄^2-, PO₄^3-), and dimethyl sulfide (DMS) concentrations. Viral communities determined by randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) were grouped according to the sampling location, being more similar within them than among regions. The first two axes of a canonical correspondence analysis, including physicochemical (temperature, salinity, inorganic nutrients-NO_3-, SiO₄^2-, and dimethyl sulfoniopropionate -DMSP- and isoprene concentrations) and microbiological (chlorophyll a, haptophytes and diatom, and prokaryote abundance and prokaryotic heterotrophic production) factors accounted for 62.9% of the variance. The first axis, temperature-related, accounted for 33.8%; the second one, salinity-related, accounted for 29.1%. Thus, different environmental situations likely select different hosts for viruses, leading to distinct viral communities.

Application of microbial network analysis to discriminate environmental heterogeneity in Fildes Peninsula, Antarctica

In order to determine the practicability of developing a protocol for bioassessing polar marine environment based on network analysis, microplankton communities and co-occurrence patterns at Ardley Cove and Great Wall Cove (King George Island, Antarctica) were studied in January 2016 through high-through sequencing. The spatial patterns and significant differences between community structures in two coves clearly reflect those in environmental heterogeneity. Moreover, both coves had their discriminated network structure and keystones. Then multivariate analyses to quantify the relationship between environmental variation and planktonic microbes response, give further evidence that nitrate and temperature, alone or in combination with other several parameters, structuring the communities respectively indeed. This study presents the first detailed description on co-occurrence networks between microbes and local environmental parameters in Antarctic coastal water. These findings suggest that co-occurrence networks based on planktonic microbes have the robust potential to assess environmental heterogeneity in polar marine ecosystem.

Correlations between biochemical composition and biogas production during anaerobic digestion of microalgae and cyanobacteria isolated from different sources of Turkey

Twenty one species of microalgae and Cyanobacteria were isolated from different ecosystems in Turkey to investigate the relation between biochemical methane potential (BMP) and biochemical characterization. Since the highest dry weight (X), specific growth rate (µ) and maximum productivity (P_max) were obtained from the five species, identification of species and BMP tests with the composition analyzes were examined. BMP values were determined 308, 293, 242, 229 and 230 mLCH₄/gVS for Desertifilum tharense, Phormidium animale, Chlorella sp., Anabeana variabilis and Chlorophyta uncultured. The Pearson correlation and principal component analysis (PCA) were applied to extract and clarify the correlation between composition of species and their methane production. Pearson correlation shows that glucose, Kjeldahl nitrogen and chlorophyll are highly and positively correlated with BMP. PCA revealed that Chlorella sp., Chlorophyta uncultured and Desertifilum tharense were placed against Phormidium animale distinguished by its extreme and different profile because of Kjeldahl nitrogen and glucose content.

Bacterial community structure in a sympagic habitat expanding with global warming: brackish ice brine at 85-90 °N

Larger volumes of sea ice have been thawing in the Central Arctic Ocean (CAO) during the last decades than during the past 800,000 years. Brackish brine (fed by meltwater inside the ice) is an expanding sympagic habitat in summer all over the CAO. We report for the first time the structure of bacterial communities in this brine. They are composed of psychrophilic extremophiles, many of them related to phylotypes known from Arctic and Antarctic regions. Community structure displayed strong habitat segregation between brackish ice brine (IB; salinity 2.4-9.6) and immediate sub-ice seawater (SW; salinity 33.3-34.9), expressed at all taxonomic levels (class to genus), by dominant phylotypes as well as by the rare biosphere, and with specialists dominating IB and generalists SW. The dominant phylotypes in IB were related to Candidatus Aquiluna and Flavobacterium, those in SW to Balneatrix and ZD0405, and those shared between the habitats to Halomonas, Polaribacter and Shewanella. A meta-analysis for the oligotrophic CAO showed a pattern with Flavobacteriia dominating in melt ponds, Flavobacteriia and Gammaproteobacteria in solid ice cores, Flavobacteriia, Gamma- and Betaproteobacteria, and Actinobacteria in brine, and Alphaproteobacteria in SW. Based on our results, we expect that the roles of Actinobacteria and Betaproteobacteria in the CAO will increase with global warming owing to the increased production of meltwater in summer. IB contained three times more phylotypes than SW and may act as an insurance reservoir for bacterial diversity that can act as a recruitment base when environmental conditions change.

Identification of Microbial Dark Matter in Antarctic Environments

Numerous studies have applied molecular techniques to understand the diversity, evolution, and ecological function of Antarctic bacteria and archaea. One common technique is sequencing of the 16S rRNA gene, which produces a nearly quantitative profile of community membership. However, the utility of this and similar approaches is limited by what is known about the evolution, physiology, and ecology of surveyed taxa. When representative genomes are available in public databases some of this information can be gleaned from genomic studies, and automated pipelines exist to carry out this task. Here the paprica metabolic inference pipeline was used to assess how well Antarctic microbial communities are represented by the available completed genomes. The NCBI's Sequence Read Archive (SRA) was searched for Antarctic datasets that used one of the Illumina platforms to sequence the 16S rRNA gene. These data were quality controlled and denoised to identify unique reads, then analyzed with paprica to determine the degree of overlap with the closest phylogenetic neighbor with a completely sequenced genome. While some unique reads had perfect mapping to 16S rRNA genes from completed genomes, the mean percent overlap for all mapped reads was 86.6%. When samples were grouped by environment, some environments appeared more or less well represented by the available genomes. For the domain Bacteria, seawater was particularly poorly represented with a mean overlap of 80.2%, while for the domain Archaea glacial ice was particularly poorly represented with an overlap of only 48.0% for a single sample. These findings suggest that a considerable effort is needed to improve the representation of Antarctic microbes in genome sequence databases.

Diversity structure of culturable bacteria isolated from the Fildes Peninsula (King George Island, Antarctica): A phylogenetic analysis perspective

It has been proposed that Antarctic environments select microorganisms with unique biochemical adaptations, based on the tenet 'Everything is everywhere, but, the environment selects' by Baas-Becking. However, this is a hypothesis that has not been extensively evaluated. This study evaluated the fundamental prediction contained in this hypothesis-in the sense that species are structured in the landscape according to their local habitats-, using as study model the phylogenetic diversity of the culturable bacteria of Fildes Peninsula (King George Island, Antarctica). Eighty bacterial strains isolated from 10 different locations in the area, were recovered. Based on phylogenetic analysis of 16S rRNA gene sequences, the isolates were grouped into twenty-six phylotypes distributed in three main clades, of which only six are exclusive to Antarctica. Results showed that phylotypes do not group significantly by habitat type; however, local habitat types had phylogenetic signal, which support the phylogenetic niche conservatism hypothesis and not a selective role of the environment like the Baas-Becking hypothesis suggests. We propose that, more than habitat selection resulting in new local adaptations and diversity, local historical colonization and species sorting (i.e. differences in speciation and extinction rates that arise by interaction of species level traits with the environment) play a fundamental role on the culturable bacterial diversity in Antarctica.

Pelagic and benthic communities of the Antarctic ecosystem of Potter Cove: Genomics and ecological implications

Molecular technologies are more frequently applied in Antarctic ecosystem research and the growing amount of sequence-based information available in databases adds a new dimension to understanding the response of Antarctic organisms and communities to environmental change. We apply molecular techniques, including fingerprinting, and amplicon and metagenome sequencing, to understand biodiversity and phylogeography to resolve adaptive processes in an Antarctic coastal ecosystem from microbial to macrobenthic organisms and communities. Interpretation of the molecular data is not only achieved by their combination with classical methods (pigment analyses or microscopy), but furthermore by combining molecular with environmental data (e.g., sediment characteristics, biogeochemistry or oceanography) in space and over time. The studies form part of a long-term ecosystem investigation in Potter Cove on King-George Island, Antarctica, in which we follow the effects of rapid retreat of the local glacier on the cove ecosystem. We formulate and encourage new approaches to integrate molecular tools into Antarctic ecosystem research, environmental conservation actions, and polar ocean observatories.