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

Potential to reduce methane production of using cultivated seaweeds supplementation to reshape the community structure of rumen microorganisms

Methane is a short-lived greenhouse gas but has a far greater warming effect than carbon dioxide. At the same time, the livestock sector serves as a large contributor to global emissions of anthropogenic methane. Herein, this work aimed to use cultivated seaweed supplementation to reduce methane emissions and investigate the potential influencing mechanism. To evaluate the feasibility, two cultivated seaweeds, Laminaria japonica Aresch, and Porphyra tenera, along with the enzymatic hydrolysates derived from L. japonica, underwent in vitro trials, and they were both added into corn silage feed (CSF) with different concentrations (1%, 5%, and 10% of CSF) for methane reduction evaluation. The results indicated that >75% and 50% reductions in methane production were observed for the seaweeds and seaweed enzymatic hydrolysates in 9- and 30-day, respectively. Combined high-throughput sequencing and multivariate analysis revealed that supplementation with seaweed and seaweed enzymatic hydrolysates had a notable impact on the prokaryotic community structure. Mantel tests further revealed that significant correlations between the prokaryotic community and methane accumulation (P < 0.05), implying the prokaryotic community plays a role in reducing methane emissions within the rumen. Correspondingly, the networks within the prokaryotic community unveiled the crucial role of propionate/butyrate-producing bacteria in regulating methane emissions through microbial interactions. The predicted function of the prokaryotic community exhibited a significant reduction in the presence of the narB gene in seaweed-supplemented treatments. This reduction may facilitate an increased rate of electron flow toward the nitrate reduction pathway while decreasing the conversion of H2 to methane. These results indicated the supplementation of cultivated seaweeds and the enzymatic hydrolysates has the potential to reshape the community structure of rumen microbial communities, and this alteration appears to be a key factor contributing to their methane production-reduction capability.

The Potential of Co-Evolution and Interactions of Gut Bacteria-Phages in Bamboo-Eating Pandas: Insights from Dietary Preference-Based Metagenomic Analysis

Bacteria and phages are two of the most abundant biological entities in the gut microbiome, and diet and host phylogeny are two of the most critical factors influencing the gut microbiome. A stable gut bacterial community plays a pivotal role in the host's physiological development and immune health. A phage is a virus that directly infects bacteria, and phages' close associations and interactions with bacteria are essential for maintaining the stability of the gut bacterial community and the entire microbial ecosystem. Here, we utilized 99 published metagenomic datasets from 38 mammalian species to investigate the relationship (diversity and composition) and potential interactions between gut bacterial and phage communities and the impact of diet and phylogeny on these communities. Our results highlight the co-evolutionary potential of bacterial-phage interactions within the mammalian gut. We observed a higher alpha diversity in gut bacteria than in phages and identified positive correlations between bacterial and phage compositions. Furthermore, our study revealed the significant influence of diet and phylogeny on mammalian gut bacterial and phage communities. We discovered that the impact of dietary factors on these communities was more pronounced than that of phylogenetic factors at the order level. In contrast, phylogenetic characteristics had a more substantial influence at the family level. The similar omnivorous dietary preference and closer phylogenetic relationship (family Ursidae) may contribute to the similarity of gut bacterial and phage communities between captive giant panda populations (GPCD and GPYA) and omnivorous animals (OC; including Sun bear, brown bear, and Asian black bear). This study employed co-occurrence microbial network analysis to reveal the potential interaction patterns between bacteria and phages. Compared to other mammalian groups (carnivores, herbivores, and omnivores), the gut bacterial and phage communities of bamboo-eating species (giant pandas and red pandas) exhibited a higher level of interaction. Additionally, keystone species and modular analysis showed the potential role of phages in driving and maintaining the interaction patterns between bacteria and phages in captive giant pandas. In sum, gaining a comprehensive understanding of the interaction between the gut microbiota and phages in mammals is of great significance, which is of great value in promoting healthy and sustainable mammals and may provide valuable insights into the conservation of wildlife populations, especially endangered animal species.

Exploring Microeukaryote Community Characteristics and Niche Differentiation in Arid Farmland Soil at the Northeastern Edge of the Tibetan Plateau

The northeastern edge of the Tibetan Plateau exhibits diverse climate and landform variations, and has experienced substantial recent environmental changes, which may significantly impact local agricultural practices. Understanding the microeukaryote community structure within agricultural soils is crucial for finding out the biological responses to such changes and may guide future agricultural practices. In this study, we employed high-throughput amplicon sequencing to examine 29 agricultural soil samples from seven research areas around the northeastern edge of the Tibetan Plateau. The findings revealed that the predominant biological communities in these soils were characterized by a high abundance of Alveolata, Amoebozoa, and Rhizaria. Ascomycota displayed the highest relative abundance among fungal communities. Moreover, notable distinctions in microeukaryote community composition were observed among the study sites. Co-occurrence network analysis highlighted interactions between the biological communities. Furthermore, our results elucidated that deterministic and stochastic processes exerted diverse influences on the distribution of protozoan and fungal communities. This study provides valuable insight into the microeukaryote structure in the agricultural soils of the northeastern edge of the Tibetan Plateau, shedding light on the intricate relationships between environmental factors, microeukaryote communities, and agricultural productivity.

Community assembly and co-occurrence network complexity of interstitial microbial communities in the Arctic (investigation of ciliates in the White Sea intertidal zone)

Arctic coastal ecosystems play a major role in global environmental system and have been altered significantly by climate changes. To better understanding the response of marine coastal ecosystems towards rapid Arctic climate changes, we examined the variation in diversity and community structure and provided insights into the co-occurrence network and community assembly of interstitial ciliates in the Kandalaksha Gulf of the White Sea from 2009 to 2019. Co-occurrence networks analysis indicated considerably high ration of positive correlations within a community that indicated low competition between interstitial ciliate species. Furthermore, we found that contribution of stochastic processes to the ciliate community assembly was insignificant. Compare with earlier data from the same ecosystem obtained in 1980s-1990s, the role of competitive factors is decreasing, and communities are becoming more spatially and temporally homogeneous. This community simplification is likely due to the response of the entire intertidal ecosystem to global climate change in Arctic.

Spatial and temporal change determined co-occurrence networks stability and community assembly processes of epipelagic seawater microbial community in the Nordic Sea

The Nordic Sea has a vital impact on the global climate change, occupies a significant status in the physical oceanography research, on account of its intersection of complex ocean currents. To explore the influence of seasonal and spatial heterogeneity in its epipelagic seawater on the microbial community structure, a total of 54 seawater samples from 18 stations and 3 water layers (0 m, 50 m, 100 m) were collected in the summer of 2017 and the autumn of 2018 from the Norwegian Sea, the Greenland Sea and the vicinity of Jan Mayen Island in the Nordic Sea. Alpha- and Beta- diversity analysis showed that significant differences were found between characteristic bacterial groups in detached or mixed currents of corresponding seasons, as endemic OTUs with seasonal and ocean current characteristics which revealed the existence of spatiotemporal patterns of microbial communities in the Nordic Sea. Moreover, co-occurrence networks were conducted to show different degree of complexity and stability of microbial community response to spatiotemporal dynamic changes. Furthermore, the flow and collision between ocean currents do have an impact on the community assembly processes by affecting the migration and dispersal of microbial communities. This study reflects the response of microbial communities to the spatiotemporal dynamics and reveals the microbial community assembly mechanisms under complex hydrological condition represented in the Nordic Sea.

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.

Spatial pattern and co-occurrence network of microbial community in response to extreme environment of salt lakes on the Qinghai-Tibet Plateau

Microbial communities are important components of alpine lakes, especially in extreme environments such as salt lakes. However, few studies have examined the co-occurrence network of microbial communities and various environmental factors in the water of salt lakes on the Qinghai-Tibet Plateau. From May to June 2019, nine samples from seven salt lakes with water salinity ranges from 13 to 267‰ on the Qinghai-Tibet Plateau were collected. There were great differences between low-salinity samples and high-salinity samples in the inorganic salt ion concentration, pH, and biodiversity. In addition, the microbial community sturcture in low-salinity samples and high-salinity samples differed, suggesting that each sample has its own specific species. The co-occurrence network suggests that salinity was the most important forcing factor. We believe that salinity and inorganic salt ions can result in differences in microbial community in different salt lakes. This sequencing survey of multiple salt lakes with various salinities on the Qinghai-Tibet Plateau enhances our understanding of the response of microbial communities to environmental heterogeneity.

Presence and distribution of triazine herbicides and their effects on microbial communities in the Laizhou Bay, Northern China

This study investigated the distribution of triazine herbicides in the Laizhou Bay, China and found that the total concentrations of triazine herbicides in the seawater and sediments were 111.15-234.85 ng/L and 0.902-4.661 μg/kg, respectively. Triazine herbicides especially ametryn, atrazine, and simazine were negatively correlated with prokaryote diversity in the seawater. While ametryn, desethylatrazine and desisopropylatrazine had positively significant effects on eukaryotes Dinophyceae, Bacillariophyta, and Cercozoa in the sediments. Moreover, the degree of fragmentation of eukaryotic networks increased dramatically with the increasing numbers of removed nodes, but prokaryotic networks did not change with the decrease of nodes. In addition, the stability analysis and neutral community models revealed that eukaryotes were more sensitive to triazine herbicides than prokaryotes. These results suggest that triazine herbicides might affect the structure and interactions of microbial communities. Therefore, more attentions should be paid to the ecological risk of triazine herbicides in marine ecosystems.

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.

Microplastics shift macrobenthic community structures near a coastal nuclear power plant under construction in North East China

Coastal sediments are considered to be a potential sink for microplastics, which mainly derived from the land-based sources. This study investigated microplastic pollution in the sediments of 20 stations near a nuclear power plant under construction in North East China and analyzed its impacts on macrobenthic communities. The average abundance of microplastics in three stations close to the nuclear power plant was 0.33 items/g, which was approximately 10 times higher than those in the distant stations. The clustering of microplastic characteristics (sizes, shapes, and colors) showed that the three stations near the plant were in one group, and the distant stations were in another group. A total of 105 macroinvertebrate species belonging to 7 phyla were identified in all stations, and the dominant phyla were Annelida and Arthropoda. Spearman rank correlation showed that rare taxa (83 species with a contribution <1 %) were positively correlated with microplastics and As, and redundancy analysis demonstrated that the distribution patterns of macrobenthic communities were similar to those of microplastics. Moreover, co-occurrence networks showed that the rare taxa were positively correlated with microplastics. Therefore, microplastics released from the nuclear power plant under construction might shift the structure of macrobenthic communities, especially the rare taxa.

Community assembly and co-occurrence network complexity of pelagic ciliates in response to environmental heterogeneity affected by sea ice melting in the Ross Sea, Antarctica

In the Southern Ocean, the living environment of organisms has changed due to the dramatic increase in melting sea ice and the loss of glaciers, which have consequently caused substantial changes in biodiversity. Samples of pelagic ciliates from 13 sites were collected as bioindicators to demonstrate the relationship between spatial distribution patterns and environmental heterogeneity affected by sea ice melting and to reveal the community assembly mechanisms in the Ross Sea. Univariate analyses and multivariate analyses were effective tools demonstrating clear spatial patterns and providing a sufficient explanation to interpret strong correlations between pelagic ciliate communities and environmental variations, especially the distribution pattern of nutrients and Chl a. Moreover, environmental heterogeneity might affect the co-occurrence network complexity of ciliate communities. Furthermore, our results also indicated that stochastic processes play a significant role in the community assembly of pelagic ciliates. This study examined the controlling mechanisms of environmental heterogeneity affected by sea ice melting on pelagic ciliate communities and provided explanations for the community assembly of pelagic ciliates in polar marine ecosystems.

Diversity and co-occurrence networks of picoeukaryotes as a tool for indicating underlying environmental heterogeneity in the Western Pacific Ocean

Picoeukaryotes are an essential component of microbial communities and play key roles in marine ecosystems. In this study, surface water picoeukaryotes were investigated at 32 stations along a latitudinal cross-section of the Western Pacific (WP) in 2015. Multivariate analyses demonstrated that there were clear spatial patterns in picoeukaryotic community structures which were consistent with the distributions of environmental variables. The spatial patterns of community structures and diversity indices were all significantly correlated with multiple environmental parameters, especially nutrients. Co-occurrence networks linked community variability to environmental heterogeneity. In summary, the construction of picoeukaryotic communities in the WP was significantly affected by numerous environmental variables, and certain variables were revealed as key forcing factors responsible for the main similarities between picoeukaryotic communities. This study details the relationships between the picoeukaryotes and environmental parameters in the WP, and provides insight for application of using picoeukaryotes as indicator in future bioassessment for open waters.

Spatial patterns and co-occurrence networks of microbial communities related to environmental heterogeneity in deep-sea surface sediments around Yap Trench, Western Pacific Ocean

Microbial communities are a large component of abyssal and hadal benthic environments, especially in deep-sea areas like Yap Trench, they provide a continuous source of nutrients and energy in their unique ecosystems. However, due to sampling difficulties, these microbial communities are relatively understudied. In the summer of 2017, sediment samples were collected from 21 stations around Yap Trench in the Western Pacific Ocean (mostly in the West Caroline Basin), at depths ranging from 3156 to 7837 m. Sediment samples from deep water depths and shallow water depths differed in organic matter content, median grain size, silt-clay content, and biodiversity. The structure of the microbial communities in the surface sediments had distinct relationships with environmental factors and their co-occurrence networks exhibited a clear spatial pattern. In addition, for both prokaryotes or eukaryotes, a combination of variables including silt-clay content, organic matter content, median grain size, and depth had the greatest impact on community structure. It was notable that fungi played important roles in the co-occurrence networks of deep water depth sediment samples while bacteria dominated those of shallow water depth samples. The differences in structure and ecological niches in the different networks were due to differences in sediment texture and organic matter content. Since clay had a positive effect on the diversity of bacteria, it had an indirect positive effect on fungi, leading to differences in biodiversity among different groups. More organic matter meant more nutrients were available for the growth and reproduction of microbes, which led to fewer niche overlaps. This study conducted an extensive and systematic sequencing survey of surface sediments around Yap Trench in the Western Pacific Ocean, providing insight into microbial responses to environmental heterogeneity in deep-sea benthic ecosystems.

Does microplastic ingestion dramatically decrease the biomass of protozoa grazers? A case study on the marine ciliate Uronema marinum

Microplastic debris has become a significant global environmental issue. Yet, the effects on ingestion of microplastics by protozoan grazers-an important link in the microbial loop-are scant. Feeding experiments were conducted with the free-living marine ciliate Uronema marinum grazing on cultured bacteria Pseudoaltermonas sp., exposing them to different concentrations or sizes of polystyrene beads for 96 h. The number of beads decreased during exposure experiments. Under the microplastic influence, the ciliate cells were observed to decrease in abundance, body size, and biomass. It was noted that the ciliate biomass in the highest microplastic density treatment was significantly lower than that in the control (98.1% lower) and that microplastics can be ingested by ciliate protozoa which performed an important role in the transportation of energy across the microbial loop. Moreover, carbon biomass of ciliates exposed to microplastics of different particle diameters decreased significantly compared to the control. However, this effect does not seem to vary depending on microplastic sizes. This study is a first step in providing experimental insight into the feeding relationship between microplastics and marine protozoan grazers. Further research based on components of the microbial loop is needed to explore the impacts of microplastics in marine food webs.

How do microplastics affect the marine microbial loop? Predation of microplastics by microzooplankton

Protozoans play an integral role in the microbial loop, an important process of material and energy transfer in marine ecosystems. The number of microplastics in the marine environment has greatly increased, but the potential impacts of small nanoplastics and microplastics on marine organisms remain unclear. Here, we conducted a series of feeding experiments with various concentrations of microplastic beads (ca. 1 μm) to characterize the response of the planktonic ciliated protozoan Strombidium sulcatum to microplastics and a set of additional exposure experiments with four different particle diameters of microplastics to explore whether the feeding response exhibited size selectivity. As the microplastic concentration increased, the number, body size, and biomass of ciliates decreased sharply during the exposure period. Predator biomass in all microplastic treatments was markedly reduced relative to the microplastic-free control. For example, at 72 h of exposure, the biomass in the highest microplastic concentration treatment was observed to decrease by 96.59% relative to the control. There was no obvious difference in the biomass of ciliates exposed to various diameters of microplastics; however, compared with the free bead control, the biomass still significantly decreased. These findings suggest that microplastics in the ocean negatively affect the growth of protozoan microzooplankton that might have accidentally ingested these tiny particles during the feeding process. Generally, this study provides basic and novel data for understanding the effect of microplastics on the microbial loop in marine ecosystems.

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.