Acidic proteomes are linked to microbial alkaline preference in African lakes.

Microbial amino acid composition (AA) reflects adaptive strategies of cellular and molecular regulations such as a high proportion of acidic AAs, including glutamic and aspartic acids in alkaliphiles. It remains understudied how microbial AA content is linked to their pH adaptation especially in natural environments. Here we examined prokaryotic communities and their AA composition of genes with metagenomics for 39 water and sediments of East African lakes along a gradient of pH spanning from 7.2 to 10.1. We found that Shannon diversity declined with the increasing pH and that species abundance were either positively or negatively associated with pH, indicating their distinct habitat preference in lakes. Microbial communities showed higher acidic proteomes in alkaline than neutral lakes. Species acidic proteomes were also positively correlated with their pH preference, which was consistent across major bacterial lineages. These results suggest selective pressure associated with high pH likely shape microbial amino acid composition both at the species and community levels. Comparative genome analyses further revealed that alkaliphilic microbes contained more functional genes with higher acidic AAs when compared to those in neutral conditions. These traits included genes encoding diverse classes of cation transmembrane transporters, antiporters, and compatible solute transporters, which are involved in cytoplasmic pH homeostasis and osmotic stress defense under high pH conditions. Our results provide the field evidence for the strong relationship between prokaryotic AA composition and their habitat preference and highlight amino acid optimization as strategies for environmental adaptation.

Soil bacteria and fungi on tropical mountainsides: Joint effects of weathering, climate, and chemical factors.

Contemporary environmental factors such as temperature and pH are generally identified as primary influences on microbial diversity, while the role of geological processes remain understudied. Here, we investigated the diversity and community composition of bacteria and fungi along an elevational gradient from703 to 4514 m on Mt. Kilimanjaro, East Africa. We further examined the effects of contemporary environment and geological processes such as weathering on microbial communities and diversities. For community composition, bacteria and fungi showed clear differentiation along elevations and their community dissimilarities increased with elevational distance indicating elevational distance-decay relationships. Multiple variables such as weathering, climate and chemical factors were significantly associated with microbial communities and showed greater effects on bacterial than fungal communities. Specifically, soil pH mainly shaped bacterial communities, while mean annual temperature for fungi, followed by other variables such as weathering processes. For Shannon diversity, bacteria and fungi showed significant hump-shaped elevational patterns with the peak values at 1857 and 1436 m, respectively. Shannon diversity was mainly affected by soil weathering accounting for 8.9% of the total variance for bacteria, while jointly by weathering and climate accounted for 14.3% of fungi. For the community uniqueness, represented by local contribution to beta diversity (LCBD), there were U-shaped patterns for both taxonomic groups. LCBD was mainly explained by the joint effects of chemical and climate variables which accounted for 51.1% and 33.4% for bacteria and fungi, respectively. Our results highlight the effects of soil weathering processes on diversity and community composition for bacteria and fungi. Thus, the integration of weathering with contemporary environments could provide new insights into microbial elevational diversity patterns.

Accuracy of ultrasound-guided fine-needle aspiration for small cervical lymph nodes: A retrospective review of 505 cases.

Purpose: The overall diagnostic value of fine-needle aspiration (FNA) is not as excellent as that of core needle biopsy (CNB). Limited research has investigated small cervical lymph nodes inaccessible to ultrasound-guided CNB due to technical challenges associated with their small size. Therefore, this study aimed to evaluate the accuracy of ultrasound-guided FNA in determining the etiology of small cervical lymph nodes. Methods: A retrospective analysis was conducted on patients who underwent FNA between May 2018 and May 2021 at our hospital. Cytological, histopathological, and clinical follow-up data were analyzed. The diagnostic yield of FNA was assessed based on sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy calculations. Results: This study included 505 patients, each with a small cervical lymph node under evaluation (total number of lymph nodes: 505). The average maximal diameter of the lymph nodes was 14.6 ± 6.2 mm. According to the Sydney system, the cytology results were as follows: Category I in 26 lymph nodes (5.1 %); Category II in 269 (53.3 %); Category III in 35 (6.9 %); Category IV in 17 (3.4 %); and Category V in 158 (31.3 %). We identified 212 malignant cases (203 metastases and 9 lymphomas) and 293 benign lymph nodes. FNA achieved high sensitivity (88.8 %), specificity (99.6 %), PPV (99.4 %), NPV (91.8 %), and overall accuracy (94.8 %) in determining the etiology of small cervical lymph nodes. Conclusion: FNA cytology is suitable for small lesions inaccessible by CNB and provides a diagnostic basis for implementing clinically appropriate treatment measures.

Sediment organic matter properties facilitate understanding nitrogen transformation potentials in East African lakes.

East African lakes include the most productive and alkaline lake group in the world. Yet, they generally receive fewer nutrient inputs than the densely populated subtropical and temperate lakes in the northern hemisphere. In these lakes with insufficient supplies of inorganic nitrogen, the mineralization of benthic organic matter can play an important role in driving the nutrient cycle and nitrogen loss. Using a suite of stable 15N isotope dilution and tracer techniques, we examined five main processes of the sediment nitrogen cycle in 16 lakes and reservoirs of Tanzania and Kenya, East Africa: gross nitrogen mineralization, ammonium immobilization, dissimilatory nitrate reduction to ammonium (DNRA), and the dinitrogen (N2) production via denitrification and anaerobic ammonium oxidation (anammox). Gross nitrogen mineralization and ammonium immobilization showed the maximum values of 9.84 and 12.39 µmol N kg-1 h-1, respectively. Potential DNRA rates ranged from 0.22 to 8.15 µmol N kg-1 h-1 and accounted for 10 %-74 % (average 25 %) of the total dissimilatory nitrate reduction. Potential nitrate reduction rates in most lakes were dominated by denitrification with a contribution of 26 %-85 % and a mean of 65 %. We further found that the sediment nitrogen transformations were driven mainly by benthic organic matter properties and water column phosphate concentrations, reflecting microbial metabolic responses to the changing carbon and nutrients availability. For instance, autochthonous production of protein-like organic matter attributed to active sediment nitrogen mineralization, DNRA, and denitrification. In contrast, the high degree of humification caused by the inputs of terrestrial humic-like substances slowed down the sediment nitrogen transformations. The contribution of DNRA to total dissimilatory nitrate reduction was significantly positively correlated to sediment C: N ratios. These results indicate that predictions of sediment N supply and loss in East African lakes can be improved by incorporating sediment organic matter properties.

Contrasting elevational patterns and underlying drivers of stream bacteria and fungi at the regional scale on the Tibetan Plateau.

Elevational gradients are the focus of development and evaluation of general theories on biodiversity. However, elevational studies of microorganisms and the underlying mechanisms remain understudied, especially at regional scales. Here, we examined stream bacterial and fungal communities along an elevational gradient of 990-4600 m with a geographic distance up to 500 km in the southeastern Tibetan Plateau and further analyzed their elevational patterns and drivers of three biodiversity indicators, including species richness, ecological uniqueness, and community composition. Bacteria and fungi showed distinct elevational trends in species richness and consistently decreasing patterns in their ecological uniqueness. The distance-decay relationships were concordant for the two microbial groups, while fungi showed higher dissimilarity and a lower turnover rate. Interestingly, bacterial and fungal compositions substantially differed between the elevations below and above 3000 m. Climate predictors, such as the mean annual temperature and precipitation seasonality, had greater effects than local environment drivers. Notably, fungal diversity was mainly influenced by climate, while bacterial diversity was explained by the shared contributions of climate and local factors. Collectively, these findings revealed the elevational patterns of stream microbial biodiversity across mountains on a large spatial scale and highlight their underlying response mechanisms to environmental predictors.

Phylogenetic divergence and adaptation of Nitrososphaeria across lake depths and freshwater ecosystems.

Thaumarchaeota (now the class Nitrososphaeria in the phylum Thermoproteota in GTDB taxonomy) are abundant across marine and soil habitats; however, their genomic diversity and evolutionary history in freshwater environments remain elusive. Here, we reconstructed 17 high-quality metagenome-assembled genomes of Nitrososphaeria from a deep lake and two great rivers, and compared all available genomes between freshwater and marine habitats regarding their phylogenetic positions, relative abundance, and genomic content. We found that freshwater Nitrososphaeria were dominated by the family Nitrosopumilaceae and could be grouped into three distinct clades closely related to the genera Nitrosopumilus, Nitrosoarchaeum, and Nitrosotenuis. The Nitrosopumilus-like clade was exclusively from deep lakes, while the Nitrosoarchaeum-like clade was dominated by species from deep lakes and rivers, and the Nitrosotenuis-like clade was mainly from rivers, deep lakes, and estuaries. Interestingly, there was vertical niche separation between two clades in deep lakes, showing that the Nitrosopumilus-like species dominated shallow layers, whereas the relative abundance of the Nitrosoarchaeum-like clade increased toward deep waters. Phylogenetic clustering patterns in the Nitrosopumilaceae supported at least one freshwater-to-marine and two marine-to-freshwater transitions, the former of which refined the potential terrestrial-to-marine evolutionary path as previously proposed. The occurrence of the two marine-to-freshwater transitions were accompanied by horizontal transfer of the genes involved in nutrition regulation, osmoregulation, and cell motility during their colonization to freshwater habitats. Specifically, the Nitrosopumilus-like clade showed losses of genes encoding flagella assembly and ion transport, whereas the Nitrosoarchaeum-like clade had losses of intact genes involved in urea uptake and utilization and gains of genes encoding osmolarity-mediated mechanosensitive channels. Collectively, our results reveal for the first time the high genomic diversity of the class Nitrososphaeria across freshwater ecosystems and provide novel insights into their adaptive mechanisms and evolutionary histories.

A few dominant bacteria and their genomic basis in mediating distinct ecosystem functions.

Species attributes such as abundance and traits are important determinant components for ecosystem functions (EFs), while their influences on distinct functions remain understudied. Here, we linked 753 treehole bacterial communities to two distinct types of EFs, including the three broad functions of respiration, metabolic activity and cell yield and the four narrow functions related to specific organic matter degradation. Towards high occurrence of phylotypes or traits, the dependency of broad EFs on species abundance or traits increased, whereas the dependency of narrow functions decreased. Among the immense number of bacterial phylotypes, the relative abundance of only 5.05% of phylotypes (that is, 542 phylotypes), but accounting for 68.60% of total abundance, were significantly related to both distinct EFs ranging from 2 to 7 functions, the level of which was used to quantify species functional generality. Such 'low species number, high relative abundance and strong functional generality' features for these 542 phylotypes could be further potentially linked to their enriched functional genes involved in cellular processes including nutrient acquisition, environmental adaptation and cell growth. Our study highlights the key role of a handful of microbial species in determining and anticipating distinct EFs by explicitly considering their abundance and trait attributes.

Microbial species performance responses to environmental changes: genomic traits and nutrient availability.

How microbial species performance indicators, such as growth rate and carbon assimilation rate, respond to environmental changes is a challenging question, especially for complex communities. This limits our ability to understand how species performance responses to environmental changes (that is, species environmental responses) of microbes could be linked to genomic traits and nutrient availability. Based on stable isotope labeling of DNA, we propose a new approach with effect-size metrics to quantify the species environmental responses of microbes by comparing the species performance between defined control and treatment groups. The species performance within microbial communities of the natural or altered environments could be quantitatively determined with quantitative stable isotope probing (qSIP). We further apply this approach, namely effect-size qSIP, to measure species environmental responses upon carbon and nitrogen additions for soil bacteria on mountainsides and to understand their responses from the perspective of genomic traits. Towards high elevations, there is a stronger nitrogen limitation that is indicated by the higher aggregated responses, measured as community-weighted means, of bacterial growth rate upon nitrogen additions. The aggregated responses are further explained by genomic traits, which show higher percentages of significant Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologues (KOs) and more diverse KEGG pathways under nutrient additions including nitrogen, and further improve the explanatory power of microbial environmental responses. Nitrogen-induced responses at the species level show the strongest associations with essential KOs for rare species, whereas carbon-induced responses show the strongest associations for dominant species. We conclude that, in addition to environmental determinants such as nitrogen limitation, genomic traits are extremely important for predicting microbial environmental responses at both the community and species levels. Taking advantage of this new approach at the species level, we reveal that rare and dominant species differentially respond to nutrient enrichment via their metabolic traits. The approach and findings can lead to a more holistic understanding of microbial environmental responses in natural habitats, which will be essential for predicting microbial community responses to global environmental changes.

Cross-taxon congruence of aquatic microbial communities across geological ages in Iceland: Stochastic and deterministic processes.

Biotic groups usually have nonrandom cross-taxon relationships in their biodiversity or compositions across sites, but it is poorly known how such congruence varies across long-term ecosystem development, and what are the ecological processes underlying biodiversity patterns. Here, we examined the cross-taxon congruence in diversity and compositions of bacteria, fungi and diatoms in streams from four regions with different geological ages in Iceland, and further studied their community assembly processes. Bacteria and fungi showed contrasting trends in alpha and gamma diversities across geological ages, while their beta diversity patterns were consistent, being the lowest in the oldest region. The three taxonomic groups had the strongest cross-taxon congruence of beta diversity in the oldest region, while the weakest for intermediate-aged regions. Although environmental variables played important roles in shaping their congruence, biotic interaction had nonnegligible influences. Deterministic processes, being dominant for bacteria and fungi, had the highest relative influence in intermediate-aged regions, whereas diatoms showed higher stochasticity. We proposed a four-phase conceptual model to show how the balance of deterministic and stochastic processes changes across geological ages. Taken together, our results provide an advanced understanding of cross-taxon congruence and community assembly processes for aquatic communities over long-term periods of geological age.

Cryptic speciation of a pelagic Roseobacter population varying at a few thousand nucleotide sites.

A drop of seawater contains numerous microspatial niches at the scale relevant to microbial activities. Examples are abiotic niches such as detrital particles that show different sizes and organic contents, and biotic niches resulting from bacteria-phage and bacteria-phytoplankton interactions. A common practice to investigate the impact of microenvironments on bacterial evolution is to separate the microenvironments physically and compare the bacterial inhabitants from each. It remains poorly understood, however, which microenvironment primarily drives bacterioplankton evolution in the pelagic ocean. By applying a dilution cultivation approach to an undisturbed coastal water sample, we isolate a bacterial population affiliated with the globally dominant Roseobacter group. Although varying at just a few thousand nucleotide sites across the whole genomes, members of this clonal population are diverging into two genetically separated subspecies. Genes underlying speciation are not unique to subspecies but instead clustered at the shared regions that represent ~6% of the genomic DNA. They are primarily involved in vitamin synthesis, motility, oxidative defense, carbohydrate, and amino acid utilization, consistent with the known strategies that roseobacters take to interact with phytoplankton and particles. Physiological assays corroborate that one subspecies outcompetes the other in these traits. Our results indicate that the microenvironments in the pelagic ocean represented by phytoplankton and organic particles are likely important niches that drive the cryptic speciation of the Roseobacter population, though microhabitats contributed by other less abundant pelagic hosts cannot be ruled out.

Mountain biodiversity and ecosystem functions: interplay between geology and contemporary environments.

Although biodiversity and ecosystem functions are strongly shaped by contemporary environments, such as climate and local biotic and abiotic attributes, relatively little is known about how they depend on long-term geological processes. Here, along a 3000-m elevational gradient with tectonic faults on the Tibetan Plateau (that is, Galongla Mountain in Medog County, China), we study the joint effects of geological and contemporary environments on biological communities, such as the diversity and community composition of plants and soil bacteria, and ecosystem functions. We find that these biological communities and ecosystem functions generally show consistent elevational breakpoints at 2000-2800 m, which coincide with Indus-Yalu suture zone fault and are similar to the elevational breakpoints of soil bacteria on another mountain range 1000 km away. Mean annual temperature, soil pH and moisture are the primary contemporary determinants of biodiversity and ecosystem functions, which support previous findings. However, compared with the models excluding geological processes, inclusion of geological effects, such as parent rock and weathering, increases 67.9 and 35.9% of the explained variations in plant and bacterial communities, respectively. Such inclusion increases 27.6% of the explained variations in ecosystem functions. The geological processes thus provide additional links to ecosystem properties, which are prominent but show divergent effects on biodiversity and ecosystem functions: parent rock and weathering exert considerable direct effects on biodiversity, whereas indirectly influence ecosystem functions via interactions with biodiversity and contemporary environments. Thus, the integration of geological processes with environmental gradients could enhance our understanding of biodiversity and, ultimately, ecosystem functioning across different climatic zones.

Trophic Status Is Associated With Community Structure and Metabolic Potential of Planktonic Microbiota in Plateau Lakes.

Microbes in various aquatic ecosystems play a key role in global energy fluxes and biogeochemical processes. However, the detailed patterns on the functional structure and the metabolic potential of microbial communities in freshwater lakes with different trophic status remain to be understood. We employed a metagenomics workflow to analyze the correlations between trophic status and planktonic microbiota in freshwater lakes on Yun-Gui Plateau, China. Our results revealed that microbial communities in the eutrophic and mesotrophic-oligotrophic lake ecosystems harbor distinct community structure and metabolic potential. Cyanobacteria were dominant in the eutrophic ecosystems, mainly driving the processes of aerobic respiration, fermentation, nitrogen assimilation, nitrogen mineralization, assimilatory sulfate reduction and sulfur mineralization in this ecosystem group. Actinobacteria, Proteobacteria (Alpha-, Beta-, and Gammaproteobacteria), Verrucomicrobia and Planctomycetes, occurred more often in the mesotrophic-oligotrophic ecosystems than those in the eutrophic ecosystems, and these taxa potentially mediate the above metabolic processes. In these two groups of ecosystems, a difference in the abundance of functional genes involved in carbohydrate metabolism, energy metabolism, glycan biosynthesis and metabolism, and metabolism of cofactors and vitamins significantly contribute to the distinct functional structure of microbiota from surface water. Furthermore, the microbe-mediated metabolic potentials for carbon, nitrogen and sulfur transformation showed differences in the two ecosystem groups. Compared with the mesotrophic-oligotrophic ecosystems, planktonic microbial communities in the eutrophic ecosystems showed higher potential for aerobic carbon fixation, fermentation, methanogenesis, anammox, denitrification, and sulfur mineralization, but they showed lower potential for aerobic respiration, CO oxidation, nitrogen fixation, and assimilatory sulfate reduction. This study offers insights into the relationships of trophic status to planktonic microbial community structure and its metabolic potential, and identifies the main taxa responsible for the biogeochemical cycles of carbon, nitrogen and sulfur in freshwater lake environments.

Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution.

Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in marine and terrestrial habitats, playing a major role in the global nitrogen cycle. However, their evolutionary history remains unexplored, which limits our understanding of their adaptation mechanisms. Here, our comprehensive phylogenomic tree of Thaumarchaeota supports three sequential events: origin of AOA from terrestrial non-AOA ancestors, colonization of the shallow ocean, and expansion to the deep ocean. Careful molecular dating suggests that these events coincided with the Great Oxygenation Event around 2300 million years ago (Mya), and oxygenation of the shallow and deep ocean around 800 and 635-560 Mya, respectively. The first transition was likely enabled by the gain of an aerobic pathway for energy production by ammonia oxidation and biosynthetic pathways for cobalamin and biotin that act as cofactors in aerobic metabolism. The first transition was also accompanied by the loss of dissimilatory nitrate and sulfate reduction, loss of oxygen-sensitive pyruvate oxidoreductase, which reduces pyruvate to acetyl-CoA, and loss of the Wood-Ljungdahl pathway for anaerobic carbon fixation. The second transition involved gain of a K+ transporter and of the biosynthetic pathway for ectoine, which may function as an osmoprotectant. The third transition was accompanied by the loss of the uvr system for repairing ultraviolet light-induced DNA lesions. We conclude that oxygen availability drove the terrestrial origin of AOA and their expansion to the photic and dark oceans, and that the stressors encountered during these events were partially overcome by gene acquisitions from Euryarchaeota and Bacteria, among other sources.

Metagenomic analysis reveals potential interactions in an artificial coculture.

Disentangling the interactions between cyanobacteria and associated bacterial community is important for understanding the mechanisms that mediate the formation of cyanobacterial blooms in freshwater ecosystems. Despite the fact that a metagenomic approach enables researchers to profile the structure of microbial communities associated with cyanobacteria, reconstructing genome sequences for all members remains inefficient, due to the inherent enormous microbial diversity. Here, we have established a stable coculture system under high salinity, originally from a mixture of an axenic cyanobacterium Synechococcus sp. PCC 7002 and a non-axenic bloom-forming cyanobacterium Microcystis colony. Metagenomic analysis showed that the coculture consists of S. sp. PCC 7002 and two heterotrophic bacteria, designated as Pseudomonas stutzeri TAIHU and Mesorhizobium sp. TAIHU, respectively. And near-complete genome sequences of both bacteria were reconstructed from the metagenomic dataset with an average completeness of 99.8%. Genome-wide pathway analysis revealed that M. sp. TAIHU carried all the genes involved in the de novo biosynthesis of cobalamin, which is required by S. sp. PCC 7002 for growth. To cope with the high salinity in the coculture, experimental evidence demonstrated that S. sp. PCC 7002 would synthesize the compatible solutes including sucrose and glucosylglycerol, which are supposed to be exploited by both heterotrophic bacteria as potential carbon and/or nitrogen sources. Furthermore, the genes encoding for the biosynthesis of the ectoine, another common osmolyte are found exclusively in P. stutzeri TAIHU, while the genes responsible for the catabolism of ectoine and its derives are present only in M. sp. TAIHU. These genomic evidence indicates beneficial interaction between three members in the coculture. Establishment of the coculture system with relative simplicity provides a useful model system for investigating the interspecies interactions, and genome sequences of both bacteria associated with Microcystis bloom described here will facilitate the researcher to elucidate the role of these heterotrophic bacteria in the formation and maintenance of cyanobacterial bloom in freshwater ecosystem.

Metagenomic Analysis Reveals Symbiotic Relationship among Bacteria in Microcystis-Dominated Community.

Microcystis bloom, a cyanobacterial mass occurrence often found in eutrophicated water bodies, is one of the most serious threats to freshwater ecosystems worldwide. In nature, Microcystis forms aggregates or colonies that contain heterotrophic bacteria. The Microcystis-bacteria colonies were persistent even when they were maintained in lab culture for a long period. The relationship between Microcystis and the associated bacteria was investigated by a metagenomic approach in this study. We developed a visualization-guided method of binning for genome assembly after total colony DNA sequencing. We found that the method was effective in grouping sequences and it did not require reference genome sequence. Individual genomes of the colony bacteria were obtained and they provided valuable insights into microbial community structures. Analysis of metabolic pathways based on these genomes revealed that while all heterotrophic bacteria were dependent upon Microcystis for carbon and energy, Vitamin B12 biosynthesis, which is required for growth by Microcystis, was accomplished in a cooperative fashion among the bacteria. Our analysis also suggests that individual bacteria in the colony community contributed a complete pathway for degradation of benzoate, which is inhibitory to the cyanobacterial growth, and its ecological implication for Microcystis bloom is discussed.

Whole-Genome Sequence of Microcystis aeruginosa TAIHU98, a Nontoxic Bloom-Forming Strain Isolated from Taihu Lake, China.

Microcystis aeruginosa is a dominant bloom-forming cyanobacterium in many freshwater lakes. This report describes the first whole-genome sequence of the nontoxic strain of M. aeruginosa TAIHU98, which was isolated from Taihu Lake in eastern China.