Abundant Species Research Articles

Examining the effect of intensive seismic surveys on abundance and behaviour of groundfish species along a continental slope of Newfoundland and Labrador, Canada.

Examining the effect of intensive seismic surveys on abundance and behaviour of groundfish species along a continental slope of Newfoundland and Labrador, Canada.

Dissolved organic matter mediates the interactions between bacterial community and heavy metal fractionation in contaminated coal mine soils.

Dissolved organic matter mediates the interactions between bacterial community and heavy metal fractionation in contaminated coal mine soils.

Centennial trends in human and climate influences on sediment-associated microorganisms in an oligotrophic lake.

Centennial trends in human and climate influences on sediment-associated microorganisms in an oligotrophic lake.

Differences in structure, antioxidant capacity and gut microbiota modulation of red raspberry pectic polysaccharides extracted by different methods.

Differences in structure, antioxidant capacity and gut microbiota modulation of red raspberry pectic polysaccharides extracted by different methods.

Investigating the bidirectional interactions between senotherapeutic agents and human gut microbiota.

Investigating the bidirectional interactions between senotherapeutic agents and human gut microbiota.

Co-occurring foundation species increase habitat heterogeneity across estuarine intertidal environments on the South Island of New Zealand.

Estuaries are traditionally considered sedimentary 'bare' ecosystems, dominated by infauna that bury into sediments to avoid being eaten by fish or birds. However, estuaries can be converted to biogenic complex 'hard' habitats, like seagrass beds, seaweed patches or surface-deposits of live or dead shells. Furthermore, habitat heterogeneity is enhanced if these foundation species co-occur. Still, few studies have quantified abundances and co-occurrences of different types of foundation species along spatiotemporal stress gradients. We therefore quantified abundances of seagrasses (Zostera muelleri), seaweeds (Ulva spp., Gracilaria chilensis), surface deposited dead shells and densities of dominant and partly buried cockles (Austrovenus stutchburyi) in estuaries on the South Island of New Zealand. A total of 927 large-scale drone images, 1264 small-scale camera images, and 160 sediment-quadrats were collected from 32 common estuarine environments (fully crossed 5-factorial surveys with 2 latitudes x 2 sites x 2 intertidal elevations x 2 seasons x 2 intra-seasonal sampling months). Across the 32 environments, seagrass was most abundant (19-22% cover, depending on sampling method), followed by shells (9-13%) and seaweed (4%). Scattered seaweed and shells were, despite their low cover, ubiquitous in the 32 environments, and seagrasses always co-occurred with shells and/or seaweed. The spatial gradients had a stronger influence on abundances of foundation species than temporal factors, that mainly affected seaweed and live cockles, with high (70%), medium (50%) and low (30%) statistical agreement between analysis of drone vs. camera images for seaweed, shells and seagrass, respectively. Finally, correlation analysis revealed negative associations between seagrasses and both shells and seaweed, but with large variation between seasons. Our study highlights that foundation species rarely occur as single-species stands, and that the ecological impacts of scattered seaweeds and dead surface-deposited shells within seagrass beds should be studied in more detail. Our findings also underscore the critical role of spatiotemporal stressors in shaping estuarine ecosystems and highlight the importance of using supplementary sampling methods to inform management strategies for estuaries in the face of environmental change.

Modified huangfeng decoction alleviates diabetic nephropathy by activating autophagy and regulating the gut microbiota.

Modified huangfeng decoction alleviates diabetic nephropathy by activating autophagy and regulating the gut microbiota.

How resilient are coastal marine soft-bottom communities with high diversity?

How resilient are coastal marine soft-bottom communities with high diversity?

Effect of Streptomyces spp. metabolites and the combination of biochar and compost on Fusarium graminearum inhibition, triticale growth, and soil properties.

Effect of Streptomyces spp. metabolites and the combination of biochar and compost on Fusarium graminearum inhibition, triticale growth, and soil properties.

Response of abundant and rare microbial species to 40-year long-term fertilization practices irrespective of bulk and rhizosphere soils.

Response of abundant and rare microbial species to 40-year long-term fertilization practices irrespective of bulk and rhizosphere soils.

Microplastic and nanoplastic exposure induced transcriptional and physiological alterations and triggered immune responses in the sea cucumber, Holothuria leucospilota.

Microplastic and nanoplastic exposure induced transcriptional and physiological alterations and triggered immune responses in the sea cucumber, Holothuria leucospilota.

Deciphering the Transformed bacterial ocular surface microbiome in diabetic mice and its Consequential influence on corneal wound healing restoration.

Deciphering the Transformed bacterial ocular surface microbiome in diabetic mice and its Consequential influence on corneal wound healing restoration.

BVOC emissions from Posidonia oceanica, the most abundant Mediterranean seagrass species.

BVOC emissions from Posidonia oceanica, the most abundant Mediterranean seagrass species.

Response of diatoms to environmental changes in the Porphyra cultivation system in Haizhou Bay using GBT model and GAM.

Response of diatoms to environmental changes in the Porphyra cultivation system in Haizhou Bay using GBT model and GAM.

Cattle grazing facilitates the species richness and abundance of temperate understory birds and alters their activity patterns

Cattle grazing facilitates the species richness and abundance of temperate understory birds and alters their activity patterns

Zooplankton community structure and vertical distribution in the South China Sea during the summer monsoon.

Zooplankton community structure and vertical distribution in the South China Sea during the summer monsoon.

Current perspective on dental black stain of bacterial origin: A narrative review.

Dental black stain is a form of external discoloration appearing as a dark line or an incomplete coalescence of dark spots in the cervical third of the tooth. This review aims to provide an up-to-date clinical and biological summary of dental black stain of bacterial origin. Black stain is esthetically unwelcome to patients, and clinicians frequently attempt its removal. Dental black plaque has a prevalence rate of 2.4%-20% affecting both genders equally and may appear throughout the lifetime. Most studies investigating the microflora of black stain reveal that Actinomyces spp. are the most abundant species found. Most authors have found a correlation between black stain and a low caries incidence. Interestingly, individuals with black stain demonstrate higher salivary concentrations of iron, sodium, copper, and calcium/phosphate, higher pH, and lower salivary flow. Standard treatment involves repeated professional ultrasonic cleaning. Alternative treatments include photo-dynamic therapy, application of virgin coconut oil, peroxide therapy, lactoferrin, or oral probiotics. Our best interpretation of the causes implicates the involvement of oral bacteria, resulting in the deposition of iron ions in patients with altered salivary composition. The use of any treatments should be balanced against potential damage to the teeth as a result of the therapy.

Relationships between mean species abundance (MSA) and potentially disappeared fraction of species (PDF) are consistent but also uncertain

Relationships between mean species abundance (MSA) and potentially disappeared fraction of species (PDF) are consistent but also uncertain

Integration of metatranscriptomics data improves the predictive capacity of microbial community metabolic models

Abstract Microbial consortia play pivotal roles in nutrient cycling across diverse ecosystems, where the functionality and composition of microbial communities are shaped by metabolic interactions. Despite the critical importance of understanding these interactions, accurately mapping and manipulating microbial interaction networks to achieve specific outcomes remains challenging. Genome-scale metabolic models (GEMs) offer significant promise for predicting microbial metabolic functions from genomic data; however, traditional community GEMs typically rely on species abundance information, which may limit their predictive accuracy due to the absence of condition-specific gene expression or protein abundance data. Here, we introduce the Integration of Metatranscriptomes Into Community GEMs (IMIC) approach, which utilizes metatranscriptomic data to construct context-specific community models for predicting individual growth rates and metabolic interactions. By incorporating metatranscriptomic profiles, which reflect both gene expression activity and partially encode abundance information, IMIC could predict condition-specific flux distributions that enable the investigation of metabolite interactions among community members. Our results show that growth rates predicted by IMIC correlate strongly with relative as well as absolute abundance of species and offer a streamlined, automated procedure for estimating the single intrinsic parameter. Specifically, IMIC results in improved predictions of measured metabolite concentration changes compared with other approaches in our case study. We further demonstrate that this improvement is driven by the network-wide adjustment of flux bounds based on gene expression profiles. In conclusion, IMIC approach enables the accurate prediction of individual growth rates and improves the model performance of predicting metabolite interactions, facilitating a deeper understanding of metabolic interdependencies within microbial communities.

Communities of Primary Producers in the Series of Reservoirs on the Sava River (Slovenia)

Different communities of primary producers were surveyed in a series of five river reservoirs on the Sava River in southeast Slovenia. Seasonal differences of phytoplanktonic and phytobenthic communities were studied in the reservoirs of hydroelectric power plants. Macrophytes were surveyed in the summer, while phytoplankton and periphyton were sampled in the winter and summer of 2021. The taxonomic composition of diatoms was studied in greater detail and additionally analysed. The results showed that the species composition of phytoplankton and phytobenthos differed between seasons. The communities were also more similar between the seasons at the same sampling site than between the sampling sites. Temperature was the parameter that had the greatest impact on the taxonomic composition of phytoplanktonic and phytobenthic communities. In total, 51 algal taxa and 81 species of diatoms were recorded, respectively. Furthermore, 15 species of aquatic macrophytes were found. The abundance of phytoplankton was the highest in the lowest reservoir in the series, in Brežice, where the temperature was also the highest. The number of macrophytes also increased downstream, but their abundances were low, mainly due to coarse substrate on the banks consisting of rocks and boulders. Constructing additional reservoirs on this section of the Sava River could increase the probability of the substantial growth of phytoplankton and cyanobacteria within it. On the other hand, providing patches of finer substrates (gravel, pebbles) would support the abundance of macrophyte species, which could control the concentrations of nutrients in the summer and prevent the blooms more efficiently.