Dominant Taxa Research Articles

Eukaryotic plankton size structure and species composition in the wetland lakes

Eukaryotic plankton play an important role in the wetland lake ecosystems. However, the size structure and species composition of eukaryotic plankton in shallow wetland lake ecosystems remains largely unexplored. To address this gap, our study employed high-throughput sequencing and quantitative PCR techniques to investigate the size structure (pico-0.7–5 μm and nano-5–20 μm) and species composition of eukaryotic plankton in two shallow wetland lakes in China during August 2016. Our findings reveal that the diversity index values of the pico-size fraction were significantly higher than those of the nano-size fraction. Additionally, there was a significant difference in community structure between these two size fractions. Furthermore, different dominant taxa were associated with each particle size, with certain lineages being enriched exclusively in one of the size fractions. In particular, biomarkers differed between the pico- and nano- fractions. The abundance of the 18S rDNA gene did not differ significantly between the two fractions. However, there was a significant difference in the abundance of gene transcripts. Moreover, the pico- fraction exhibited a significantly higher rRNA: rDNA ratio compared to the nano- fraction. It is important to note that certain taxa had lower absolute abundance in specific samples, despite their higher relative abundance.

Trophic level plays an enhanced role in shaping microbiota structure and assembly in lakes with decreased salinity on the Qinghai-Tibet and Inner Mongolia Plateaus

Plateau lakes characterized by salinization and eutrophication are essential aquatic ecosystems. A myriad of microorganisms serve as crucial biological resources in plateau lakes and drive the elemental cycles of these ecosystems. Currently, there is a paucity of knowledge regarding the impacts of salinization and eutrophication dynamics on the microbiota in plateau lakes. Here, high-throughput sequencing of the 16S ribosomal RNA genes (V4 region) was used to characterize microbial community structure and assembly in plateau lakes with different salinities and trophic levels. Water samples were collected at 191 sites across 24 lakes on the Qinghai-Tibet and Inner Mongolia Plateaus in northern China. The results showed that high salinity considerably reduced microbial alpha-diversity and niche breadth while increasing within-group similarity among various lake types. High salinity additionally decreased the complexity of microbial networks and enhanced network robustness. The assembly of microbial communities was primarily governed by deterministic processes in high-salinity and eutrophic low-salinity lakes. At decreased salinity, trophic level played a leading role in shaping microbial community structure, and the ecological processes shifted from deterministic processes driven by high salinity to eutrophication-driven deterministic processes. The biomarkers also varied from taxa adapted to high-salinity environments (e.g., Nanoarchaeaeota, Rhodothermia) to those suited for living in freshwater and low-salinity habitats (e.g., Alphaproteobacteria, Actinobacteria). In the case of eutrophication, Actinobacteria, Chloroflexi, and Cyanobacteria became the dominant taxa. Our findings indicate that decreased salinity enables trophic level to play an enhanced role in shaping microbial community structure and assembly in plateau lakes. This study enriches our knowledge about the ecological impacts of salinization and eutrophication in plateau lakes.

The zooplankton community of Baltic Sea ports: diversity and seasonal dynamics

In this study, we investigated zooplankton composition and seasonal dynamics, as well as the influence of selected environmental factors on the zooplankton community in three ports on the Polish Baltic coast: Władysławowo, Gdynia and Gdańsk. Our aim was to determine whether harbours’ heavy traffic, chemical pollution and physical disturbances affect the zooplankton community, and whether new nonindigenous planktonic species occur in these habitats. Forty three zooplankton taxa were found in all three ports; however, it is important to note that no new nonindigenous species were observed in the port basins. The most influential environmental factors affecting the zooplankton community were: seawater temperature (17% of explained zooplankton variability) and transparency (4%), which were related to seasonal changes. Acartia spp. (although of different development stages) was the dominant taxon during the study, and the examined ports/seasons differed in the presence and proportions of less abundant taxa: the autumn and winter assemblages were dominated by Acartia spp. nauplii, the spring assemblage by numerous Polychaeta larvae, while Cirripedia nauplii and early development stages of Eurytemora affinis were particularly abundant in summer. In addition, changes in salinity (2% explained variability) had a particular impact on the zooplankton community and especially on the assemblage of Gdańsk Port, which was influenced by freshwater inflow from the Motława and Dead Vistula rivers. Our study has clearly shown that, despite severe physical and chemical disturbances in all studied ports, the composition and seasonal dynamics of the zooplankton community were similar to those of the Gulf of Gdańsk outside the ports.

Short-term effects of substrate surface structure on macroinvertebrates community structure and functional characteristics

Stones are one of the important natural materials in soil bioengineering and are widely used in river ecosystem restoration projects. After stones are introduced into the river channel, they become a crucial component of the riverbed substrate. Substrate is a crucial habitat for macroinvertebrates. The surface structure of substrate plays a vital role in providing habitat for a greater diversity of macroinvertebrates, thus contributing significantly to the enhancement of riverine biodiversity. This study was conducted in the headwater streams of Changbai Mountain. Complexity was introduced to the substrate surface by adding rough treatments on concrete blocks, as well as different sizes of grooves and holes. The study found that the control substrate (GK0/GT0) took the shortest time (7 d) to establish a relatively stable macroinvertebrate community. In contrast, other treated substrates required a longer time to form relatively stable communities due to the increased available living space on the substrate surface. Overall, various diversity indices were relatively higher on rough substrates compared to smooth substrates. Specifically, at 28 d, the groove-treated substrate MT1 had the highest species richness (18.67) and Shannon-Wiener diversity index (H′, 2.85), which were 2.68 times and 1.54 times higher than the control, respectively. Similarly, at 28 d, the hole-treated substrate MK1 exhibited the highest species richness (20.35) and H′ (2.84), which were 2.90 times and 1.53 times higher than the control, respectively. With the gradient changes in groove and hole sizes, macroinvertebrate species richness, density, H′, Margalef richness index (dM), and Simpson dominance index (D) on different substrates showed an initial increase followed by a decrease trend. Additionally, attached organisms were the dominant taxa on all treated substrates, with higher densities of burrowers in hole-treated substrates and more swimmers in groove-treated substrates. Substrates with larger holes favored the settlement of larger-bodied macroinvertebrates, while substrates with small grooves had higher abundances of various-sized macroinvertebrate groups. It is evident that differences in substrate surface structure have a significant impact on macroinvertebrate diversity and functional characteristics. Therefore, in river ecosystem restoration projects, adding necessary textural structures to the substrate surface can enhance the effectiveness of river ecosystem restoration.

Arsenic biomineralization and selenium nanoparticles biosynthesis by Halomonas boliviensis strain H-10 isolated from the high-altitude Salar de Huasco salt flat (Chile)

High-altitude Andean wetlands of the Atacama Desert (Chile), including the Salar de Huasco salt flat, are unusual environments characterized by a great variability of physical-chemical conditions, often combined with a high concentration of heavy metals, including arsenic (As) and semimetals, such as selenium (Se). Microorganisms present in these environments evolved adaptative strategies to cope with environmental stresses, with biotechnological potentials. The present work investigated the natural bacterial community composition in sediments collected from the Salar de Huasco salt flat, by high-throughput Illumina sequencing, and to isolate bacterial strains able to remove As and biosynthesize Se nanoparticles (SeNPs). Dominant taxonomic groups (abundance ≥1%) were affiliated to Proteobacteria (mainly consisting in Delta- and Alfa- Gamma-proteobacteria) Bacteriodetes, Firmicutes, Acidobacteria, Spirochaetes, Deinococcus-Thermus, Gemmatimonadetes and Verrucomicrobia. Halomonas boliviensis strain H-10 was able to both biomineralize As and biosynthesise SeNPs; therefore, the characteristics of H. boliviensis strain H-10 could be used for biotechnological purposes, including As bioremediation from water and bioproduction of SeNPs.

Ostracoda and Foraminifera as bioindicators of (aquatic) pollution in the protected area of uMlalazi estuary, South Africa

To mitigate ecological and health risks, implementing a comprehensive multidisciplinary monitoring strategy is imperative. This approach aims to effectively identify and record potential declines in water quality and ecological conditions. Utilizing cost-effective and efficient monitoring tools is crucial, especially for developing nations. Despite the previously reported uMlalazi River's pristine status within a protected natural reserve at South Africa's eastern coast, our findings challenge the assumption of its cleanliness, emphasizing the need for ongoing proactive monitoring. Here we reassess the pollution levels and ecological status of aquatic life of the river, and use this to enhance the indicator value of microfauna in South Africa. We analysed 25 surface sediment samples from the uMlalazi estuary, covering a salinity range from oligohaline to euhaline, with a focus on marginal marine Ostracoda and Foraminifera as potential indicators. All samples contained Ostracoda and Foraminifera, with the exception of two. Among the identified ostracod species, there were 17 species belonging to 14 genera. Typical taxa are the brackish water species Perissocytheridea estuaria, Sulcostocythere knysnaenis, and Australoloxoconcha favornamentata. We identified 19 Foraminifera species from 16 genera, with dominant taxa such as Ammonia sp., Quinqueloculina sp., and Miliolinella sp. Three distinct assemblages were observed: A) Ammonia sp. and Quinqueloculina sp., with very low diversity and abundances in general, located along the river course at stations exceeding Pollution Load Index (PLI), which indicates deterioration of sites quality; B) Ammonia sp., Quinqueloculina sp., and Sulcostocythere knysnaenis associated with higher salinity and lower PLI; C) Ammonia sp., Quinqueloculina agglutinans, and Cribroelphidium articulatum located in mudflats with minimal PLI. Our findings align with the commonly observed diversity trend, which indicates reduced species diversity corresponding to elevated pollution levels. Notably, the examined samples revealed a range of Foraminiferal Abnormality Index (FAI) up to 23%, exhibiting anomalies such as multiple tests, changes in coiling, and abnormal chamber shapes. Geochemical analysis indicates that the catchment is subjected to substantial anthropogenic pressure, as evidenced by elevated concentrations of heavy metals, sulphur, and microplastic. Sugarcane farming, urban sewage, titanium mining, and fish farming are the primary sources of pollution in the catchment area. Ongoing investigations in South African estuaries are expanding our dataset and will contribute to a better understanding of the species-specific responses of Ostracoda and Foraminifera to anthropogenic pressure.

The phoD-Harboring Microorganism Communities and Networks in Karst and Non-Karst Forests in Southwest China

Phosphorous (P) limitation is common not only in tropical rainforest and savanna ecosystems, but also in karst forest ecosystems. Soil phoD-harboring microorganisms are essential in soil P cycles, but very little information is available about them in karst ecosystems. A total of 36 soil samples were collected from two types of forest ecosystems (karst and non-karst) over two seasons (rainy and dry), and the diversity and community structure of soil phoD-harboring microorganisms were measured. The contents of available P (AP), soil total P (TP), microbial biomass P (MBP) and the activity of alkaline phosphatase (ALP) in karst forest soils were higher than those in non-karst forest soils, whereas the contents of CaCl2-P, citrate-P, enzyme-P and the activity of acid phosphatase (ACP) were the opposite. Soil AP content was significantly higher in the rainy season than in the dry season, whereas ALP activity was the opposite. The community structure of phoD-harboring microorganisms was more influenced by forest-type than season. The network connectivity was higher in non-karst forests than in karst forests. Two dominant orders, Burkholderiales and Rhizobiales, were the keystone taxa in these networks in two forests, and their relative abundances were higher in non-karst forests than in karst forests. The microorganic diversity indices (e.g., Shannon–Wiener, Evenness, Richness, and Chao1) were substantially higher in karst than in non-karst forests. These indices were positively correlated with the contents of SOC and TN in the two forests; meanwhile, richness and evenness indices were positively correlated with citrate-P, HCl-P, and TP in non-karst forests. Structural equation modelling results showed that the relative abundance of phoD-harboring microorganisms was mainly influenced by pH and AP, with direct affection of soil AP, pH, and ALP activity, and indirect affection of ALP activity through affecting AP. These findings highlight that the P cycle is mainly regulated by the diversity of phoD-harboring microorganisms in karst forest ecosystems, whereas it is mainly regulated by dominant taxa in non-karst forest ecosystems. In future, regulating the interaction networks and keystone taxa of phoD-harboring microorganisms may be critical to alleviating P limitations in karst forest ecosystems.

Characterization of an undocumented CO2 hydrothermal vent system in the Mediterranean Sea: Implications for ocean acidification forecasting.

A previously undocumented shallow water hydrothermal field from Sicily (Southern Tyrrhenian Sea, Italy) is here described, based on a multidisciplinary investigation. The field, covering an area of nearly 8000 m2 and a depth from the surface to -5 m, was explored in June 2021 to characterise the main physico-chemical features of the water column, describe the bottom topography and features, and identify the main megabenthic and nektonic species. Twenty sites were investigated to characterise the carbonate system. Values of pH ranged between 7.84 and 8.04, ΩCa between 3.68 and 5.24 and ΩAr from 2.41 to 3.44. Geochemical analyses of hydrothermal gases revealed a dominance of CO2 (98.1%) together with small amounts of oxygen and reactive gases. Helium isotope ratios (R/Ra = 2.51) and δ13CCO2 suggest an inorganic origin of hydrothermal degassing of CO2 and the ascent of heat and deep-seated magmatic fluids to the surface. Visual census of fishes and megabenthos (mainly sessile organisms) allowed the identification of 64 species, four of which are protected by the SPA/BIO Protocol and two by the International Union for Conservation of Nature. The macroalgae Halopteris scoparia and Jania rubens and the sponge Sarcotragus sp. were the dominant taxa in the area, while among fishes Coris julis and Chromis chromis were the most abundant species. This preliminary investigation of San Giorgio vent field suggests that the site could be of interest and suitable for future experimental studies of ocean acidification.

Morphology of ctenostome bryozoans: 7. Hislopia, Echinella andTimwoodiellina.

Ctenostome bryozoans are a small group of gymnolaemates comprising less than 400 recent species. They are paraphyletic and ctenostome-grade ancestors gave rise to Cheilostomata, the most dominant and speciose taxon of Bryozoa in the present day. Investigations into ctenostomes are important for reconstructing character evolution among Gymnolaemata. As a continuation of studies on a morphological series of ctenostome bryozoans, we herein investigate six species of hislopiids, a small clade of threegenera occurring in freshwater habitats. The general morphology of all species is similar in having primarily uniserial chains of encrusting zooids, which are mostly oval to ellipsoid and have a flattened frontobasal axis. Hislopia prolixa and Echinella placoides often have more slender zooids with a higher frontobasal axis. Apertures of hislopiids are quadrangular, lined by a thickened cuticle. Apertural spines are present in various lengths in E. placoides, Hislopia lacustris and Hislopia corderoi. The remaining cuticle is rather thin except at lateral areas, close to the pore-plates which are prominent in hislopiids because of abundant special and limiting cells. All species except H. corderoi and Timwoodiellina natans have a prominent collar obstructing the vestibulum, whereas the latter two species instead have an 'external collar' as cuticular, outer folds projecting over the aperture. Hislopiid lophophores carry eight, or more commonly 12-18 tentacles. The digestive tract is distinguished by an often highly elongated esophagus and/or cardia, with the latter always having a prominent bulbous part in the form of a proventriculus-or gizzard in E. placoides. The caecum is extensive in all species. In Hislopia the intestine is characteristically two-chambered with a proximal and distal part before entering an anal tube of various length. The latter is present in all species except T. natans and terminates in mid-lophophoral area. Oocytes in E. placoides are large and macrolecithal indicating brooding and the production of lecithotrophic larvae. Hislopia species produce small, oligolecithal ones, which suggests zygote spawning and planktotrophy. In general, the morphology is similar among the different hislopiids with characters of the gut aiding in delineating the genera Echinella and Timwoodiellina.

Characteristics of Groundwater Microbial Community Composition and Environmental Response in the Yimuquan Aquifer, North China Plain

To explore the intricate interrelationship between groundwater microbial communities and hydrochemical characteristics in the Mancheng District, Baoding City, samples from karst groundwater and porous groundwater were collected. Hydrochemical analysis and the 16s RNA gene V4-V5 region sequencing method were used to detail the water environmental characteristics and microbial community distribution pattern in the study area. The hydrochemical results reveal notable differences in major ion contents and other hydrochemical indices between karst water and porous water. Microbial community analysis demonstrates that Proteobacteria, Actinobacteria, and Firmicutes are the dominant taxa in both types of water bodies, albeit with significant variations in their proportions across distinct water bodies. The observed disparities in microbial communities between karst water and porous water underscore the influence of environmental factors such as ion concentration and pH on microbial distribution. Redundancy Analysis (RDA) indicates notable associations between microbial community composition and environmental factors in both types of groundwater environments. Studying the distribution pattern of microbial communities and the connection with environmental factors in two types of groundwater lays a crucial foundation for interpreting the functional roles of microbes in groundwater ecosystems.

The Investigation of Changes in Bacterial Community of Pasteurized Milk during Cold Storage

The quality of pasteurized milk is commonly assessed through microbiological analysis, with variations in storage conditions significantly impacting the suppression of bacterial growth throughout the milk’s shelf life. This study investigated the dynamics of total bacterial counts (TBCs) and bacterial community shifts in milk that underwent pasteurization at 80 °C for 15 s. The milk was subsequently stored at 4 °C for varying intervals of 1, 4, 7, 10, 13, and 16 days. Culture-based testing revealed a significant TBC increase during the storage period spanning 1 to 16 days (up to −log10 4.2 CFU/mL at day 16). The TBC in pasteurized milk exhibited accelerated microbial growth from day 13 onwards, ultimately peaking on day 16. Bacillus was detected through 16S rRNA identification. Principal component analysis demonstrated a significant impact of storage time on bacterial communities in pasteurized milk. Analysis of bacterial diversity revealed a negative correlation between the Shannon index and the duration of pasteurized milk storage. Using high-throughput sequencing, Streptococcus and Acinetobacter were detected as prevalent bacterial genera, with Streptococcus dysgalactiae and Streptococcus uberis showing as dominant taxa. The presence of Streptococcus dysgalactiae and Streptococcus uberis in pasteurized milk might be attributed to the initial contamination from raw milk with mastitis. This study offers new evidence of the prevalence of bacterial community in pasteurized milk, thereby adding value to the enhancement of quality control and the development of strategies for reducing microbial risks.

Host plants directly determine the α diversity of rhizosphere arbuscular mycorrhizal fungal communities in the National Tropical Fruit Tree Field Genebank

Arbuscular mycorrhizal fungi (AMF) typically exhibit reduced diversity in nutrient-rich soils. However, whether the influence of host plants on AMF within the rhizosphere is direct or indirect through the alteration of soil nutrient levels has yet to be determined. This study explored the diversity and colonization of AMF in the National Tropical Fruit Tree Genebank, where chemical fertilizers are used to preserve minor tropical fruit germplasms. We aimed to understand the direct and indirect effects of host plants on AMF community dynamics, sporulation, and colonization. By analyzing fine roots and rhizosphere soil from 12 tropical fruit trees, we assessed mycorrhizal colonization indices, soil nutrients, AMF spore density, and community structure. Despite their low colonization density and arbuscular abundance, all the tree roots harbored AMF, with spore densities ranging from 24.00 to 204.80 spores/100 g of dry soil. High-throughput sequencing identified 207 AMF virtual taxa (VTs) from 60 soil samples, with dominant taxa, including early-evolved Paraglomus fungi and ruderal AMF, being minimally affected by soil nutrient levels. Interestingly, there was no correlation between α diversity and spore density. Structural equation modeling (SEM) indicated that host plant evolutionary divergence time (ET) directly influenced AMF α diversity indices and indirectly impacted spore density via soil nutrients. However, neither ETs nor soil nutrients significantly affected the AMF community structure, with only arbuscular abundance showing a negative correlation with ET. This research underscores the intricate relationship between host plants and AMF in genebanks, offering insights for effective AMF resource management and informed conservation practices.Graphical

Variability of marine epifauna assemblages in response to the microhabitat type and thermal stress

Anthropogenic activities like overfishing, urban and industrial developments, and coastal pollution are some of the stressors affecting the marine environment. Thermal pollution from coastal industries like power plants represents the main cause of increased temperatures in water bodies, which can affect the marine community structure and function. The aim of this study was: 1) to compare the epifaunal communities associated with three different types of microhabitats: articulated coralline algae around coral colonies (CWC), articulated coralline algae in the absence of coral colonies and other benthic organisms (CNB), and the seaweed Ecklonia cava (ECK); and 2) to determine the potential changes in epifaunal communities in acute response to the increased water temperature resulting from coastal power plant activities in Jeju Island, South Korea. Our findings revealed a strong association between epifaunal abundance and microhabitat type, with CNB exhibiting the highest abundance while ECK showed the lowest. Additionally, an increase in temperature of 0.5–1.5 °C was observed to not alter the overall abundance of epifauna at the impact site, however, it did lead to a shift in the community composition. There was a notable decline in the abundance of amphipods-caprellids, polychaetes, gastropods, and bivalves with their densities nearly halving in response to thermal stress. Furthermore, there was a shift in dominant taxa, transitioning from amphipods-caprellids to amphipods-non-caprellids. Conversely, other taxonomic groups such as isopods and copepods showed a remarkable surge in abundance following the temperature rise. These findings highlight the relationship between rising temperatures and epifaunal community composition while emphasizing taxa’s different responses to thermal stress.

Meiofauna community structure in the Yellow Sea Cold Water Mass and non‐Yellow Sea Cold Water Mass

This study investigated meiofaunal community structure over a large area of the Yellow Sea and East China Sea for 45 stations from 2021 to 2022. Meiofaunal densities were 34 ± 15–1610 ± 378 ind./10 cm2. Nematodes (67.3%) were the most dominant taxa, followed by benthic foraminifera (12.0%) and benthic harpacticoids (8.8%). The study was conducted in various sedimentary environments. Median grain size, water depth, and environmental characteristics (TOC, TN, Hg, Sr) were identified as influencing meiofauna community structure. The Yellow Sea and East China Sea, where this study was conducted, contain a variety of currents and the Yellow Sea Cold Water Mass (YSCWM) in the central waters. YSCWM and non-YSCWM areas differed in their meiofauna community structure. Even within the YSCWM region, we found differences in benthic community structure due to a variety of environmental factors. The meiofaunal taxon most affected by Sediment temperature was benthic foraminifera. Identifying foraminifera in paleo-oceanographic environments can indicate past expansion and contraction of YSCWM. Meiofauna have been used to monitor changes in marine ecosystems due to their sensitivity to changes in the surrounding environment. Meiofauna index (N/C ratio, MPI) were identified as appropriate for use in the study area.

Effects of Aquaculture and Thalassia testudinum on Sediment Organic Carbon in Xincun Bay, Hainan Island

Eutrophication due to aquaculture can cause the decline of seagrasses and impact their carbon storage capacity. This study explored the effects of aquaculture on the sediment organic carbon (SOC) in Thalassia testudinum seagrass beds using enzyme activity and microorganisms as indicators. Our results showed that the distance to aquaculture significantly increased the SOC and TN of sediments; the C/N ratio of sediments was reduced by the distance to aquaculture. Distance to aquaculture and seagrasses significantly impacted the δ13C of sediments, and their significant interactive effects on the δ13C of sediments were found. Distance to aquaculture and seagrasses had significantly interactive effects on the cellulase activity of sediments. Distance to aquaculture and seagrasses separately reduced the invertase activity of sediments. SOC in the seagrass bed was significantly positively impacted by cellulase activity and polyphenol oxidase activity in sediments. Firmicutes, Desulfobacterota and Chloroflexi were the dominant taxa in the S1 and S2 locations. From the S1 location to the S2 location, the relative abundances of Firmicutes and Desulfobacterota increased. The functional profiles of COG were relatively similar between the S1 and S2 locations. BugBase phenotype predictions indicated that the microbial phenotypes of all the seagrass sediment samples were dominated by anaerobic bacteria in terms of oxygen utilizing phenotypes. FAPROTAX functional predictions indicated that aquaculture affects functions associated with seagrass bed sediment bacteria, particularly those related to carbon and nitrogen cycling. This study can provide an important basis for understanding the response mechanism of global carbon sink changes to human activities such as aquaculture and supply more scientific data for promoting the conservation and management of seagrass beds.

Unraveling the role of bacterial communities in mangrove habitats under the urban influence, using a next-generation sequencing approach

Mangrove ecosystems are vital coastal habitats with rich biodiversity and play a significant role in carbon sequestration, these habitats are facing mounting threats from rapid urbanization. This study delves into assessing the sediment bacterial communities from the urban mangrove habitats of Campal and Panaji, within the Mandovi estuarine environment of Goa, to understand the intricate interplay between urbanization and bacterial dynamics in the mangrove habitats. We used a combined approach of 16S amplicon and shotgun sequencing methodologies to understand the bacterial taxonomic composition and functional profiles. The community structure revealed the dominance of bacterial groups from phylum Proteobacteria, Chloroflexi and Actinobacteria at both locations. The impact of urbanization was evident from the increased abundance of pathogenic groups at class and genus levels in this region. The core microbiome analysis showed the presence of Shewanella, Pseudomonas and Clostridium which are mostly pathogenic, anaerobic taxa Woeseia, Rheinheimera, like genera that are involved in the organic matter cycling and unclassified bacteria. Though increased pathogenic forms are reported, it is evident that the dominant taxa also included groups that contributed to the biogeochemical cycling of organic matter in sediment from these locations. Functional diversity elucidated through shotgun metagenomics analysis showcased the predominance of carbohydrate metabolism and the presence of glycoside hydrolases degrading plant-based starch, pectin and cellulosic organic matter. The occurrence of xenobiotic biodegradation pathways is an indication of the presence of xenobiotic degrading microbes as a natural means of degrading high amounts of pollutants at this location. Comparative analysis of the metagenomes from this study with similar earlier studies at Ribandar, Mandovi and Cortalim, Zuari mangrove habitats of Goa with varying pollution levels also reiterates the terrestrial influence on the microbial community in these habitats. It showed that Panaji and Campal locations had the presence of dominant pathogenic forms which was absent in the other two locations. The Ribandar and Coratlim location which is reported to have a comparatively lesser impact due to anthropogenic activity had an increased abundance of distinct genera which are predominant heterotrophic forms involved in remineralization and reduced levels of pathogens. Our findings highlight the profound influence of urbanization on the sediment mangrove bacterial communities and spotlight the resilience and adaptability of these microorganisms. This calls for immediate action and preventive measures to restore their functional potential in maintaining the health of these ecosystems amidst expanding urban landscapes.

Assembly of cereal crop fungal communities under water stress determined by host niche

Crop-associated fungi play an important role in agroecosystems. However, a comprehensive understanding of the ecological mechanisms governing fungal community assembly is lacking. Here, we established a wheat (Triticum aestivum) and oat (Avena sativa) cropping system and sampled crop associated fungal communities under different water stresses. The results show that fungal community assembly in the soil-plant continuum is mainly determined by host niches rather than water stress and genotype. However, within the same host niche, water stress and genotype significantly influenced the assembly of fungal communities. This finding was further supported by the network complexity and dissimilarity-overlap analysis. Epiphytes and leaf endosphere exhibited a complex network structure, characterized by strong positive interactions among the members of the mycobiome. The network complexity of the phylloplane increased under drought stress. The analysis of microbial source tracking revealed that the fungi in the roots primarily originated from the bulk soil, while most fungi in the leaves originated from unknown sources under different water stress. In addition, crop mycobiome was governed by a few dominant taxa, with Sordariomycetes identified as an important biomarker taxon for roots and Trichosporonales for leaves. This study provides comprehensive empirical evidence on the assembly mechanisms of crop fungal communities.

Community structure and association network of prokaryotic community in surface sediments from the Bering-Chukchi shelf and adjacent sea areas.

The Bering-Chukchi shelf is one of the world's most productive areas and characterized by high benthic biomass. Sedimentary microbial communities play a crucial role in the remineralization of organic matter and associated biogeochemical cycles, reflecting both short-term changes in the environment and more consistent long-term environmental characteristics in a given habitat. In order to get a better understanding of the community structure of sediment-associated prokaryotes, surface sediments were collected from 26 stations in the Bering-Chukchi shelf and adjacent northern deep seas in this study. Prokaryote community structures were analyzed by metabarcoding of the 16S rRNA gene, and potential interactions among prokaryotic groups were analyzed by co-occurrence networks. Relationships between the prokaryote community and environmental factors were assessed. Gammaproteobacteria, Alphaproteobacteria, and Flavobacteriia were the dominant bacterial classes, contributing 35.0, 18.9, and 17.3% of the bacterial reads, respectively. The phototrophic cyanobacteria accounted for 2.7% of the DNA reads and occurred more abundantly in the Bering-Chukchi shelf. Prokaryotic community assemblages were different in the northern deep seas compared to the Bering-Chukchi shelf, represented by the lowered diversity and the increased abundant operational Taxonomic Units (OTU), suggesting that the abundant taxa may play more important roles in the northern deep seas. Correlation analysis showed that latitude, water depth, and nutrients were important factors affecting the prokaryote community structure. Abundant OTUs were distributed widely in the study area. The complex association networks indicated a stable microbial community structure in the study area. The high positive interactions (81.8-97.7%) in this study suggested that symbiotic and/or cooperative relationships accounted for a dominant proportion of the microbial networks. However, the dominant taxa were generally located at the edge of the co-occurrence networks rather than in the major modules. Most of the keystone OTUs were intermediately abundant OTUs with relative reads between 0.01 and 1%, suggesting that taxa with moderate biomass might have considerable impacts on the structure and function of the microbial community. This study enriched the understanding of prokaryotic community in surface sediments from the Bering-Chukchi shelf and adjacent sea areas.

Land use effects on soil microbiome composition and traits with consequences for soil carbon cycling.

The soil microbiome determines the fate of plant-fixed carbon. The shifts in soil properties caused by land use change leads to modifications in microbiome function, resulting in either loss or gain of soil organic carbon (SOC). Soil pH is the primary factor regulating microbiome characteristics leading to distinct pathways of microbial carbon cycling, but the underlying mechanisms remain understudied. Here, the taxa-trait relationships behind the variable fate of SOC were investigated using metaproteomics, metabarcoding, and a 13C-labeled litter decomposition experiment across two temperate sites with differing soil pH each with a paired land use intensity contrast. 13C incorporation into microbial biomass increased with land use intensification in low-pH soil but decreased in high-pH soil, with potential impact on carbon use efficiency in opposing directions. Reduction in biosynthesis traits was due to increased abundance of proteins linked to resource acquisition and stress tolerance. These trait trade-offs were underpinned by land use intensification-induced changes in dominant taxa with distinct traits. We observed divergent pH-controlled pathways of SOC cycling. In low-pH soil, land use intensification alleviates microbial abiotic stress resulting in increased biomass production but promotes decomposition and SOC loss. In contrast, in high-pH soil, land use intensification increases microbial physiological constraints and decreases biomass production, leading to reduced necromass build-up and SOC stabilization. We demonstrate how microbial biomass production and respiration dynamics and therefore carbon use efficiency can be decoupled from SOC highlighting the need for its careful consideration in managing SOC storage for soil health and climate change mitigation.

Rainfall-induced changes in aquatic microbial communities and stability of dissolved organic matter: Insight from a Fen river analysis

Microbial communities are pivotal in aquatic ecosystems, as they affect water quality, energy dynamics, nutrient cycling, and hydrological stability. This study explored the effects of rainfall on hydrological and photosynthetic parameters, microbial composition, and functional gene profiles in the Fen River. Our results demonstrated that rainfall-induced decreases in stream temperature, dissolved oxygen, pH, total phosphorus, chemical oxygen demand, and dissolved organic carbon concentrations. In contrast, rainfall increased total dissolved solids, salinity, and ammonia-nitrogen concentrations. A detailed microbial community structure analysis revealed that Cyanobacteria was the dominant microbial taxon in the Fen River, accounting for approximately 75% and 25% of the microalgal and bacterial communities, respectively. The abundance of Chlorophyta and Bacillariophyta increased by 47.66% and 29.92%, respectively, whereas the relative abundance of Bacteroidetes decreased by 37.55% under rainfall conditions. Stochastic processes predominantly affected the assembly of the bacterial community on rainy days. Functional gene analysis revealed variations in bacterial functions between sunny (Sun) and rainy (Rain) conditions, particularly in genes associated with the carbon cycle. The 3-oxoacyl-[acyl-carrier-protein] reductase gene was more abundant in the Fen River bacterial community. Particular genes involved in metabolism and environmental information processing, including the acetyl-CoA C-acetyltransferase (atoB), enoyl-CoA hydratase (paaF), and branched-chain amino acid transport system gene (livK), which are integral to environmental information processing, were more abundant in Sun than the Rain conditions. In contrast, the phosphate transport system gene, the galactose metabolic gene, and the pyruvate metabolic gene were more abundant in Rain. The excitation-emission matrix analysis with parallel factor analysis identified four fluorescence components (C1–C4) in the river, which were predominantly protein- (C1) and humic-like (C2–C4) substances. Rainfall affected organic matter production and transport, leading to changes in the degradation and stability of dissolved organic matter. Overall, this study offers insight into how rainfall affects aquatic ecosystems.