Diatom cell-size composition is an indicator of aquatic environmental changes but has been rarely investigated, especially in semi-terrestrial peatlands. In this study, both taxonomic composition and cell-size composition of diatoms were analysed in 41 samples from two montane peatlands, northeastern China. Redundancy analyses revealed that diatom taxonomic composition was significantly related to the depth to the water table (DWT) and Ca2+, while cell-size composition was significantly associated with DWT and Si. DWT was the most important factor and its sole effect explained 26.2% and 17.9% of the total variance in taxonomic composition and cell-size composition, respectively. Accordingly, diatom-based water-table transfer functions were developed based on taxonomic composition and cell-size composition, respectively. The maximum-likelihood (ML) model based on diatom taxonomic composition had the best performance, with a correlation coefficient value (R2) of 0.78 and the root mean squared error of prediction (RMSEP) of 6.66 cm. The ML model based on cell-size composition had similar performance, with an R2 of 0.78 and the RMSEP of 6.87 cm, suggesting that diatom cell-size composition can be a new quantitative means to track past water-table changes. This method requires further appraisal with palaeoecological data but offers a new option that deserves exploration.

Historically, our understanding of bacterial ecology in the Indian Ocean has been limited to regional studies that place emphasis on community structure and function within oxygen minimum zones. Thus, bacterial community dynamics across the wider Indian Ocean are largely undescribed. As part of Bio-GO-SHIP, we sequenced the 16S rRNA gene from 465 samples collected on sections I07N and I09N. We found that (i) there were 23 distinct bioregions within the Indian Ocean, (ii) the southeastern gyre had the largest gradient in bacterial alpha-diversity, (iii) the Indian Ocean surface microbiome was primarily composed of a core set of taxa, and (iv) bioregions were characterized by transitions in physical and geochemical conditions. Overall, we showed that bacterial community structure spatially delineated the surface Indian Ocean and that these microbially-defined regions were reflective of subtle ocean physical and geochemical gradients. Therefore, incorporating metrics of in-situ microbial communities into marine ecological regions traditionally defined by remote sensing will improve our ability to delineate warm, oligotrophic regions.

Modern microbial mats are relictual communities mostly found in extreme environments worldwide. Despite their significance as representatives of the ancestral Earth and their important roles in biogeochemical cycling, research on microbial mats has largely been localized, focusing on site-specific descriptions and environmental change experiments. Here, we present a global comparative analysis of non-lithifying microbial mats, integrating environmental measurements with metagenomic data from 62 samples across eight sites, including two new samples from the recently discovered Archaean Domes from Cuatro Ciénegas, Mexico. Our results revealed a notable influence of environmental filtering on both taxonomic and functional compositions of microbial mats. Functional redundancy appears to confer resilience to mats, with essential metabolic pathways conserved across diverse and highly contrasting habitats. We identified six highly correlated clusters of taxa performing similar ecological functions, suggesting niche partitioning and functional specialization as key mechanisms shaping community structure. Our findings provide insights into the ecological principles governing microbial mats, and lay the foundation for future research elucidating the intricate interplay between environmental factors and microbial community dynamics.

Over the last decades, the analysis of complex microbial communities by high-throughput sequencing of marker gene amplicons has become routine work for many research groups. However, the main challenges faced by scientists who want to make use of the generated sequencing datasets are the lack of expertise to select a suitable pipeline and the need for bioinformatics or programming skills to apply it. Here, we present MetaXplore, an interactive, user-friendly platform that enables the discovery and visualization of amplicon sequencing data. Currently, it provides a set of well-documented choices for downstream analysis, including alpha and beta diversity analysis, taxonomic composition, differential abundance analysis, identification of the core microbiome within a population, and biomarker analysis. These features are presented in a user-friendly format that facilitates easy customization and the generation of publication-quality graphics. MetaXplore is implemented entirely in the R language using the Shiny framework. It can be easily used locally on any system with R installed, including Windows, Mac OS, and most Linux distributions, or remotely via a web server without bioinformatic expertise. It can also be used as a framework for advanced users who can modify and expand the tool.

In this study, two different approaches based on taxonomic assemblages and on copepod functional groups were used to investigate the mesozooplankton assemblage structure and its relationship with environmental variables in the main estuaries of the Gulf of Cádiz (Guadalquivir, Guadiana and Tinto-Odiel) during the dry-warm season. In general, the mesozooplankton assemblages were dominated by copepods, especially the calanoid Acartia tonsa, which reached its highest abundance in the inner zones while the adjacent coastal zones were characterized by a mixture of copepods and cladocerans, especially Penilia avirostris. Regarding the trait-based approach, three copepod functional groups were identified, principally sorted by their feeding strategy. Group 1 (composed of omnivorous copepods displaying a mixed feeding strategy and broadcast-spawners) was found mainly in the inner areas, while Groups 2 (omnivorous cyclopoids, sac-spawners that feed via active ambush) and 3 (herbivores-omnivores employing a filter feeding strategy and mostly broadcast-spawners) were predominant in the adjacent coastal zones. The relative abundance of copepod functional groups suggested that Group 1 could be considered the most important contributor to secondary production in the estuarine systems of the Gulf of Cádiz. In relation to environmental factors, salinity was the most influential variable on mesozooplankton assemblages in both approaches. Our results suggest that the studied estuaries, although taxonomically different, have mesozooplankton assemblages that perform similar ecological functions. Both methods provide valuable and complementary information about mesozooplankton assemblage dynamics in the main estuaries of the Gulf of Cádiz.

Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) is a traditional non-culture technique that can provide a fingerprint of the microbial community. In the field of gut microbiota analysis, PCR-DGGE still holds potential for development. In the present study, we utilized an improved nested PCR-DGGE approach targeting the V3 region of 16S ribosomal DNA to investigate the impact of whole grain highland hull-less barley (WHLB), a cereal known for its significant hypocholesterolemic effect, on the gut microbiota profiles of high-fat diet rats. Seventy-two male Sprague-Dawley rats were divided into four groups and fed a normal control diet, a high-fat diet, or a high-fat diet supplemented with a low or high dose of WHLB for 4 or 8 weeks. The results revealed that the dominant bands varied among different dose groups and further changed with different treatment times. The compositions of bacterial communities in feces and cecal content were similar, but the dominant bacterial bands differed. After performing double DGGE, extracting the bands, sequencing the DNA, and aligning the sequences, a total of 19 bands were classified under the Firmicutes and Bacteroidetes phyla, while two bands were identified as unclassified uncultured bacteria. The relative abundance of Lactobacillus gasseri, Uncultured Prevotella sp., and Clostridium sp. increased following the administration of WHLB. Illumina-based sequencing was employed to assess the reliability of DGGE, demonstrating its reliability in analyzing the dominant taxonomic composition, although it may have limitations in accurately detecting the alpha diversity of bacterial species.
OBJECTIVE: While next-generation sequencing has overshadowed polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), the latter still holds promise for advancing gut microbiota analysis due to its unique advantages. In this study, we used optimized nested PCR-DGGE to investigate the gut microbiota profile of high-fat diet rats after administering whole grain highland hull-less barley. High-throughput sequencing was employed to validate the DGGE results. Our results proved the reliability of PCR-DGGE for analyzing the dominant taxonomic composition while also providing visual evidence of a notable relationship between the composition of cecal and fecal microbial communities, highlighting substantial differences in both richness and abundance.

Recent studies have shown that the bacterial microbiome of the respiratory tract influences the development of lung cancer. Changes in the composition of the microbiome are observed in patients with chronic inflammatory processes. Such microbiome changes may include the occurrence of bacteria that cause oxidative stress and that are capable of causing genome damage in the cells of the host organism directly and indirectly. To date, the composition of the respiratory microbiome in patients with various histological variants of lung cancer has not been studied. In the present study, we determined the taxonomic composition of the sputum microbiome of 52 patients with squamous cell carcinoma of the lung, 52 patients with lung adenocarcinoma and 52 healthy control donors, using next-generation sequencing (NGS) on the V3-V4 region of the bacterial gene encoding 16S rRNA. The sputum microbiomes of patients with different histological types of lung cancer and controls did not show significant differences in terms of the species richness index (Shannon); however, the patients differed from the controls in terms of evenness index (Pielou). The structures of bacterial communities (beta diversity) in the adenocarcinoma and squamous cell carcinoma groups were also similar; however, when analyzed according to the matrix constructed by the Bray-Curtis method, there were differences between patients with squamous cell carcinoma and healthy subjects, but not between those with adenocarcinoma and controls. Using the LEFse method it was possible to identify an increase in the content of Bacillota (Streptococcus and Bacillus) and Actinomycetota (Rothia) in the sputum of patients with squamous cell carcinoma when compared with samples from patients with adenocarcinoma. There were no differences in the content of bacteria between the samples of patients with adenocarcinoma and the control ones. The content of representatives of the genera Streptococcus, Bacillus, Peptostreptococcus (phylum Bacillota), Prevotella, Macellibacteroides (phylum Bacteroidota), Rothia (phylum Actinomycetota) and Actinobacillus (phylum Pseudomonadota) was increased in the microbiome of sputum samples from patients with squamous cell carcinoma, compared with the control. Thus, the sputum bacterial microbiome of patients with different histological types of non-small-cell lung cancer has significant differences. Further research should be devoted to the search for microbiome biomarkers of lung cancer at the level of bacterial species using whole-genome sequencing.
Исследования последних лет показали, что бактериальный микробиом респираторного тракта влияет на развитие рака легкого. Изменение состава микробиома у пациентов связывают с хроническими воспалительными процессами, так как многие бактерии вызывают окислительный стресс, а также способны прямо или опосредованно повреждать геном в клетках организма хозяина. До настоящего времени состав респираторного микробиома у больных с различными гистологическими вариантами рака легкого не изучен. В настоящем исследовании для анализа таксономического состава микробиома мокроты 52 пациентов с плоскоклеточным раком легкого, 52 пациентов с аденокарциномой легкого и 52 здоровых доноров контрольной группы использовали технологию массового параллельного секвенирования региона V3-V4 16S рРНК. Микробиомы мокроты больных с разными гистологическими типами рака легкого и контроля не имели значимых различий по индексу видового богатства (Шеннона), однако у пациентов они отличались от контроля по индексу выравненности (Пиелу). Структуры бактериальных сообществ (бета-разнообразие) между аденокарциномой и плоскоклеточным раком также были близкими. Тем не менее матрица, построенная по Брэю–Кёртису, позволила выявить различия между пациентами с плоскоклеточным раком и здоровыми субъектами, но не между аденокарциномой и контролем. Метод LEFse позволил идентифицировать в мокроте больных плоскоклеточным раком увеличение содержания Bacillota (Streptococcus и Bacillus) и Actinomycetota (Rothia) при сопоставлении с образцами пациентов с аденокарциномой. Не найдено различий в содержании бактерий между образцами больных аденокарциномой и контроля. В микробиоме образцов мокроты пациентов с плоскоклеточным раком по сравнению с контролем было повышено содержание представителей родов Streptococcus, Bacillus, Peptostreptococcus (филум Bacillota), Prevotella, Macellibacteroides (филум Bacteroidota), Rothia (филум Actinomycetota) и Actinobacillus (филум Pseudomonadota). Таким образом, бактериальный микробиом мокроты пациентов с разными гистологическими типами немелкоклеточного рака легкого имеет существенные различия. Дальнейшие исследования должны быть посвящены поиску микробиомных биомаркеров рака легкого на уровне бактериальных видов с использованием полногеномного секвенирования.

Soil microbiota, which plays a fundamental role in ecosystem functioning, is sensitive to environmental changes. Studying soil microbial ecological patterns can help to understand the consequences of environmental disturbances on soil microbiota and hence ecosystem services. The different habitats with critical environmental gradients generated through the restoration of coal-mining subsidence areas provide an ideal area to explore the response of soil microbiota to environmental changes. Here, based on high-throughput sequencing, we revealed the patterns of soil bacterial and fungal communities in habitats with different land-use types (wetland, farmland, and grassland) and with different restored times which were generated during the ecological restoration of a typical coal-mining subsidence area in Jining City, China. The α-diversity of bacterial was higher in wetland than in farmland and grassland, while that of fungi had no discrepancy among the three habitats. The β-diversity of bacterial community in the grassland was lower than in the farmland, and fungal community was significant different in all three habitats, showing wetland, grassland, and farmland from high to low. The β-diversity of the bacterial community decreased with restoration time while that of the fungal community had no significant change in the longer-restoration-time area. Furthermore, soil electrical conductivity was the most important driver for both bacterial and fungal communities. Based on the taxonomic difference among different habitats, we identified a group of biomarkers for each habitat. The study contributes to understand the microbial patterns during the ecological restoration of coal-mining subsidence areas, which has implications for the efficient ecological restoration of subsidence areas.

Wastewater treatment plants (WWTP) are essential infrastructure in our developing world. However, with the development and release of novel entities and without modern upgrades, they are ineffective at fully removing micropollutants before treated effluents are released back into aquatic environments. Thus, WWTPs may represent additional point source impacts to freshwater environments, further pressuring aquatic fauna and already vulnerable insect communities. Previous studies - mostly focusing on single WWTPs - have shown general trends of freshwater invertebrate communities becoming dominated by pollution tolerant taxa. To expand on these findings, the current study is the first to comprehensively investigate data on the effects of 170 WWTPs on invertebrate taxonomic composition. We compared data for several diversity and pollution indices, as well as the taxonomic composition both upstream and downstream of the WWTPs (366 sampling sites). In terms of abundance, the three most frequent and negatively impacted orders were the Plecoptera, Trichoptera and Gastropoda, while the Turbellaria, Hirudinea and Crustacea increased in abundance. Although strong changes in community composition were observed between upstream and downstream sites (mean species turnover of 61%), commonly used diversity indices were not sensitive to these changes, highlighting their potential inadequacy in accurately assessing ecological health. Our results indicate that WWTPs change downstream conditions in favour of pollution tolerant taxa to the detriment of sensitive taxa. Order-level taxonomic responses can be informative but should be interpreted with caution, since they can be driven by a few taxa, or opposing responses of species in the same group can result in an overall low order-level response. Upgrading WWTPs via additional treatment steps or merging may be beneficial, provided upstream sections are unimpacted and/or are in a good chemical and structural condition.

Free-living marine nematodes are valuable biological indicators for different environmental disturbances. Their taxonomic composition and functional traits often respond to environmental changes. In this study, marine nematodes, collected from the Bohai sea on the northeastern coast of China in 2014, were investigated in terms of their taxonomic composition and functional traits. Furthermore, the environmental quality of the investigated area was assessed based on nematode metrics. The studied nematode community showed spatial variation in taxonomic and functional composition, in response to changes in environmental variables such as sediment chlorophyll-a, phaeophytin-a, organic matter content, silt-clay content etc. Overall, high percentage of tolerant marine nematodes species or colonizers predominated, suggesting a disturbed environmental condition of the study area. Further results from the environmental quality assessment based on nematode metrics indicated a moderate quality status at the most investigated stations.