Tiny unicellular cyanobacteria or picocyanobacteria (0.5–3 µm) are important due to their ecological significance. Chesapeake Bay is a temperate estuary that contains abundant and diverse picocyanobacteria. Studies of Chesapeake Bay picocyanobacteria in the past 20 years led to the finding of new members of subcluster 5.2 Synechococcus. They laid the foundation for revealing the ecophysiology, biogeography, genomics, and molecular evolution of picocyanobacterial in the Chesapeake Bay and other coastal estuaries. The Bay picocyanobacteria are known to better tolerate the changes in temperature, salinity, and heavy metals compared to their coastal and open-ocean counterparts. Many picocyanobacteria isolated from the Bay contain rich toxin–antitoxin (TA) genes, suggesting that the TA system may provide them with a genetic advance to cope with variable estuarine environments. Distinct winter and summer picocyanobacteria are present in the Bay, suggesting a dynamic seasonal shift of the picocyanobacterial community in the temperate estuary. While the Bay contains subcluster 5.2 Synechococcus, it also contains freshwater Synechococcus, Cyanobium, and marine Synechococcus due to river influx and the ocean’s tidal influence. Some Chesapeake Bay picocyanobacterial clades were found in the Bering Sea and Chukchi Sea, showing a link between the Bay and polar picocyanobacteria. Genomic sequences of estuarine picocyanobacteria provide new insight into the taxonomy and evolution of freshwater, estuarine, and marine unicellular cyanobacteria. Estuaries connect freshwater and marine ecosystems. This overview attempts to extend what we learned from Chesapeake Bay picocyanobacteria to picocyanobacteria in freshwater and marine waters.
Traditional cultivation methods with defined growth media can only isolate and cultivate a small number of microbes. However, much higher microbial diversity has been detected by cultivation-independent tools from a range of natural ecosystems. These represent a large unexplored pool of potentially novel taxa. In this study, a diffusion-based integrative cultivation approach (DICA) was developed to efficiently isolate novel taxonomic candidates from marine sediment. DICA combined a newly designed diffusion-based apparatus called a “microbial aquarium” with modified low-nutrient media. To determine the efficiency of DICA, cultivation results were compared with traditional cultivation approach (TCA). Both cultivation approaches resulted in the isolation of numerous representatives from the phyla Pseudomonadota, Actinomycetota, Bacteroidota, and Bacillota. However, the newly developed DICA also led to the successful cultivation of species from rarely cultivated phyla such as Verrucomicrobiota and Balneolota. Based on 16S rRNA analyses, the application of DICA resulted in the successful cultivation of 115 previously uncultured taxa out of a total of 196 isolates. Among these, 39 were identified at the genus level and 4 at the family level, showcasing a novelty ratio of 58%. Conversely, the TCA cultivated 12% (20/165) of novel isolates, with all at species level only. The isolated microbial diversity showed that species recovered by DICA belong to 12 different classes, twice the number produced by TCA. Overall, these results demonstrate that the newly designed DICA produces a high recovery of diverse and previously uncultured bacteria.
Marine heterotrophic prokaryotes initially release extracellular enzymes to cleave large organic molecules and then take up ambient substrates via transporters. Given the direct influence of extracellular enzymes on nutrient availability, understanding their diversity and dynamics is crucial in comprehending microbial interactions and organic matter cycling in aquatic ecosystems. In this study, metagenomics was employed to investigate the functional diversity and dynamics of extracellular enzymes and transporters in coastal waters over a 22-day period. The metagenome-derived gene pool of organic matter-degrading secretory enzymes and transporters was primarily contributed by three major bacterial classes. Bacteroidota were the primary contributors to the gene pool of secretory carbohydrate-active enzymes (CAZymes), whereas Gammaproteobacteria contribute more to secretory peptidases and TonB-dependent transporters (TBDTs), and Alphaproteobacteria to ATP-binding cassette (ABC) transporters. The distinct substrate targets of the enzymes and transporters combined with the unique dynamics of these taxa across depth layers suggest that organic matter degradation and uptake machinery played a role in ecological niche partitioning. At the community level, the abundance of TBDT genes was more positively correlated with extracellular enzymes than ABC transporters. To further explore taxon-specific differences, we reconstructed 163 bacterial and archaeal metagenome-assembled genomes (MAGs). Correlation patterns at the MAG level varied across taxa: Bacteroidota MAGs exhibited significant positive correlations between TBDTs and extracellular enzymes, whereas Gammaproteobacteria and Alphaproteobacteria MAGs showed weak or no significant correlations. These results suggest the diversity of ecological strategies among marine heterotrophic bacteria and highlight a potential coregulation or functional linkage between extracellular enzymes and TBDTs in the metabolism of marine heterotrophic prokaryotes. Our study advances the understanding of the microbial adaptations driving carbon and nutrient cycling.
Special Topic: Ecology & Environmental Biology.
The online version contains supplementary material available at https://doi.org/10.1007/s42995-025-00314-9.
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
Microbial degradation of methylphosphonate (MPn) is an important pathway contributing to the ‘methane paradox’ in the oxic ocean. Vibrio spp. are suggested to participate in this process. However, little is known about the molecular basis, phylogenetic breadth and catabolic efficiency of methane production in Vibrio species. Here, 18 Vibrionales strains known to be effective in MPn demethylation were obtained. The most effective strains, i.e., Vibrio gallaecicus HW2-07 and HW2-08, can convert 70%–80% of amended MPn into methane in 5 days. Estimations based on quantitative PCR determination indicated that Vibrio spp. were influential contributors to marine methane production. Genes flanking the common phn genes suggested a divergent gene arrangement and grouped the phn operons into nine types. This was consistent with the phylogeny of phnJ and phnL. The phn operons of cluster I and II were identified frequently in Vibrio isolates and were common in coastal seas and the open ocean. Addition of MPn increased expression of the phn genes, as well as an unexpected gene that encodes an acyltransferase (act), which frequently occurred in cluster I–IV operons. This study provided experimental evidence and theoretical support for a further understanding that Vibrio spp. may play important roles in aerobic marine methane production.
Special Topic: Ecology & Environmental Biology.
The online version contains supplementary material available at https://doi.org/10.1007/s42995-025-00278-w.
Anaerobic ammonium oxidation (anammox) plays a critical role in nitrogen loss in estuarine and marine environments. However, the mechanisms underlying the formation and maintenance of the anammox bacterial community remain unclear. This study analyzed the anammox bacterial diversity, community structure, and interspecific relationships in three estuaries along the Chinese coastline —the Changjiang Estuary (CJE), the Oujiang Estuary (OJE), and the Jiulong River Estuary (JLE) — as well as the South China Sea (SCS) to elucidate their community assembly mechanisms. The results indicated that the anammox bacterial community exhibited the highest ammonium concentration as well as the Shannon’s diversity index reflecting both species richness and evenness in the JLE. The lowest Shannon index was observed in the SCS. However, the anammox bacterial species richness was greatest in the CJE. Candidatus Scalindua was the predominant anammox bacteria identified in the coastal sediments, especially in the SCS sediments. Candidatus Brocadia and Candidatus Kuenenia were more abundant in the estuarine sediments, particularly in JLE, than in the SCS. Phylogenetic analysis revealed distinct differentiation among Candidatus Scalindua, Candidatus Brocadia, and Candidatus Kuenenia, with the former exhibiting a greater level of diversity. There was significant spatial heterogeneity in the anammox bacteria across the four regions, characterized by distinct distribution patterns for rare species. Low-abundance (rare) bacteria thrived in their native habitats, whereas abundant taxa displayed greater dispersal capabilities. An analysis of the community assembly mechanism suggested that ecological drift predominantly shaped the overall anammox bacterial community in the coastal sediments. Rare species were more susceptible to dispersal limitations and environmental selection. Co-occurrence network analysis identified Candidatus Scalindua as a keystone genus and highlighted that rare species may play a crucial role in maintaining the ecological stability of the anammox bacterial community in coastal sediments.
Special Topic: Ecology & Environmental Biology.
The online version contains supplementary material available at https://doi.org/10.1007/s42995-025-00315-8.
CO2 concentration mechanisms (CCMs) are important in maintaining the high efficiency of photosynthesis of marine algae. Aquatic photoautotrophs have two types of CCMs: biophysical CCMs, based on the conversion of inorganic carbon, and biochemical CCMs, based on the formation of C4 acid intermediates. However, the contribution of biophysical and biochemical CCMs to algal carbon fixation remains unclear. Here, we used ethoxyzolamide (EZ) inhibitors of carbonic anhydrase and 3-mercaptopicolinic acid (MPA) inhibitors for phosphoenolpyruvate carboxykinase to examine the importance of biophysical and biochemical CCMs in photosynthesis of the green macroalga Ulva prolifera. The culture experiments showed that the carbon fixation of the species declined when EZ inhibited the biophysical CCM, while the increase in cyclic electron flow around the photosystem I indicated a more active biochemical CCM, contributing to ~ 50% of total carbon fixation. The biophysical CCM was also reinforced when MPA inhibited the biochemical CCM. In a comparison, the biophysical CCM can compensate for almost 100% of total carbon fixation. The results indicate that biophysical CCMs dominate the process of carbon fixation of U. prolifera while biochemical CCM plays a supporting role. Our results provide evidence of a complementary coordination mechanism between the biophysical and biochemical CCMs that promotes the efficiency of photosynthesis of U. prolifera, an efficient mechanism to boost the alga’s bloom.
Special Topic: Ecology & Environmental Biology.
The online version contains supplementary material available at https://doi.org/10.1007/s42995-024-00265-7.
Habitat fragmentation is a major cause of biodiversity loss. Fragmentation can alter thermal conditions on the remaining patches, especially at habitat edges, but few studies have examined variations in thermal tolerance of species in fragmented habitats. Ants are sensitive to both habitat fragmentation and temperature changes, and are an ideal taxon for studying these impacts. Here, we focused on the dimorphic ant species Pheidole nodus in a fragmented habitat island system (Thousand island lake) in China. We assessed critical thermal maximum (CTmax), minimum (CTmin), and range (CTrange) temperatures for both minor (workers) and major workers (soldiers) of 2307 individuals from 117 edge and interior colonies across 9 islands during relatively hot and cold seasons. Using mixed-effect linear models, we explored the effects of island area, habitat type (edge vs. interior), season, and caste (worker vs. soldier) on CTmax, CTmin, and CTrange. We found temperatures were 1–3 °C higher in edge than interior sites in relatively hot season. Yet, only CTmax and CTrange in edge populations were higher than those of interior sites on smaller islands. CTmax was higher in relatively hot season and CTmin was lower in relatively cold season, indicating seasonal plasticity in thermal tolerance. Workers consistently had higher CTmax and lower CTmin than soldiers. These findings underscore the importance of seasonality, worker caste, and interactive effect between island area and habitat type in shaping thermal tolerance of a dominant dimorphic ant species on fragmented habitat islands. Our study provides a roadmap for integrating thermal biology into studies of how fragmentation impacts biodiversity.
Special Topic: Ecology & Environmental Biology.
The online version contains supplementary material available at https://doi.org/10.1007/s42995-025-00288-8.
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
The queen snapper (Etelis oculatus Valenciennes in Cuvier & Valenciennes, 1828) is a deep-sea snapper whose commercial importance continues to increase in the US Caribbean. However, little is known about the biology and ecology of this species. In this study, the presence of a fine-scale population structure and genetic diversity of queen snapper from Puerto Rico was assessed through 16,188 SNPs derived from the Restriction site Associated DNA Sequencing (RAD-Seq) technique. Summary statistics estimated low genetic diversity (HO = 0.333–0.264) and did not reveal population differentiation within our samples (FST = − 0.001–0.025). Principal component analysis and a model-based clustering method did not detect a fine-scale subpopulation structure among sampling sites, however, there was genetic variability within regions and sites. Our results have revealed comparable genetic and dispersal patterns to those observed in other shallow-water snapper species in Puerto Rico waters. It is crucial to further enhance our understanding of the ecological and biological aspect of the queen snapper to effectively manage and conserve this species as fishing pressure has been extended to deep water species in the US Caribbean.
Special Topic: Ecology & Environmental Biology.
The online version contains supplementary material available at https://doi.org/10.1007/s42995-025-00289-7.
The distribution of Pampus argenteus (Euphrasen, 1788) spans a pronounced latitudinal–environmental gradient from the subtropical to the subpolar zones. The species is reported to have multiple stocks along coastal China, exhibiting different spawning behaviors and habitat preferences. Such ecological variations might imply potential genetic divergence and local adaptation. We resequenced 117 genomes from six coastal stocks of P. argenteus in China. Although no hierarchical genetic structure was identified, over 50% of the single-nucleotide polymorphisms (SNPs) indicated moderate to strong divergence in at least two stocks. The Mantel test identified 21 100-kb sliding windows with significant isolation by distance and environment, while a majority did not. Given the lack of genome-wide isolation by distance, the 21 windows may be under selection pressure from the latitudinal–environmental variations. Among the 21 windows, certain genes were linked to circadian clock regulation and thermal stress response, suggesting sea surface temperature and sunshine duration as selective forces. A total of 17 genes regulated neuron activity; variations near these genes might subsequently shape the different spawning and migratory behaviors among the stocks. Additionally, 1204 SNPs were mapped to non-coding regions; 14 transcriptional and translational factors were identified in the 21 windows. These findings imply that alterations in gene expression might contribute to the local adaptation of the P. argenteus stocks.
Special Topic: Ecology & Environmental Biology.
The online version contains supplementary material available at https://doi.org/10.1007/s42995-025-00312-x.
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
Mongolian gerbils had high ability to endure both high and cold temperatures. To study the mechanism of high ability for thermal adaptation, gerbils were acclimated to high temperature (30 °C) for 8 weeks, and were measured for metabolic features, body composition as well as mitochondrial content and activities. Lipidomic techniques were used to measure changes in mitochondrial membrane, including potential mitochondrial membrane remodeling during acute thermoregulation in gerbils. Heat acclimated gerbils showed lower basal metabolic rates but no changes in adaptive non-shivering thermogenesis were detected. A significant mitochondrial membrane remodeling with increases in monounsaturated/polyunsaturated free fatty acids ratios was associated with the decrease in metabolic rate. During heat acclimation, mitochondrial cytochrome C oxidase activity was elevated in brown adipose tissue, presumably caused by the increase in membrane unsaturation. Our results indicated that mitochondrial membrane remodeling is an important mechanism during heat acclimation in Mongolian gerbils, to reduce the metabolic rate in general while preserving sufficient capability to respond to acute cold. Such a mechanism may allow gerbils to cooperate with wide range of daily and seasonal temperature fluctuations.
Special Topic: Ecology & Environmental Biology.
The online version contains supplementary material available at https://doi.org/10.1007/s42995-025-00317-6.
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.