Differences In Community Structure Research Articles

Nematode community structure suggests perennial grain cropping cultivation as a nature‐based solution for resilient agriculture

AbstractIntroductionConventional agricultural land‐use may negatively impact biodiversity and the environment due to the increased disturbances to the soil ecosystem by tillage, for example. Cultivation of the perennial grain intermediate wheatgrass (Thinopyrum intermedium, IWG, Kernza®) is a nature‐based solution for sustainable agriculture, improving nutrient retention mainly through its extensive root system. Nematodes serve as sensitive bioindicators, detecting early changes in the soil food web, reflecting in changes in their community structure.Materials and MethodsIWG and annual wheat sites in South France, Belgium and South Sweden were investigated in April 2022 for two depths (5–15 cm; 25–35 cm) to evaluate the difference in nematode community structure among the cropping systems.ResultsSites with IWG cultivation held an accumulation of structure indicators (c‐p 3–5 nematodes) compared to sites with annual wheat cultivation. A generalised linear mixed model revealed significantly more root feeders, especially for the subsoil, under IWG as a result of the perennial cultivation. The maturity index, plant‐parasitic index, channel index and structure index were greater for IWG sites. The enrichment index was greater for annual wheat sites due to the dominance of bacterivores and enrichment indicators (c‐p 1 nematodes). The nematode community structure (weighted faunal profile analysis) indicates IWG sites as being a generally undisturbed system with efficient nutrient cycling and balanced distribution of feeding types, as well as higher metabolic footprint values for root feeders (including plant‐parasitic nematodes) and fungivores. Annual wheat sites, on the other hand, held indicators of a disturbed system with increased occurrence of opportunistic species and a more bacterial driven pathway. The topsoil had an increased occurrence of structure indicators in both cropping systems.ConclusionIWG creates favourable conditions for a diverse food web, including improved nutrient cycling and a heterogeneous resource environment, regardless of climatic conditions, establishing it as a stable and resilient agricultural management system.

Spatio-temporal dynamics of phytoplankton community structure in the coastal waters of the Southern Beibu Gulf.

This study was conducted during October 2021 (autumn) and April 2022 (spring) to explore the phytoplankton community structure, their distribution characteristics, and the influence of environmental factors in the coastal waters of the Southern Beibu Gulf. The 15 sampling sites were grouped based on the difference in offshore distance to analyze the temporal and spatial differences in community structure and environmental driving in the investigated sea area of the coastal waters of the Southern Beibu Gulf. Permutational multivariate analysis of variance was conducted on the sample data in time and space, revealing that there is no significant difference in space (p > 0.05), but there is significant difference in time (p < 0.05). Notably, water pressure, pH, chemical oxygen demand, nitrite, and labile phosphate were higher in autumn, while total ammonia nitrogen, dissolved oxygen, and suspended solids were significantly higher in spring. Additionally, the study identified 87 phytoplankton species belonging to 6 phyla, dominating by Bacillariophyta, followed by Dinophyta and Cyanophyta. The phytoplankton density, Shannon Weiner's diversity index (H'), Pielou's evenness index (J), and Margalef's richness index (D) ranged from 84.88 to 4675.33 cells L-1, 0.56 to 2.58, 0.26 to 0.89, and 1.21 to 3.64, respectively. Permutational multivariate analysis of variance showed non-significant spatial differences in phytoplankton composition (p > 0.05) but seasonal differences (p < 0.05). Furthermore, canonical correspondence analysis (CCA) identified pH, dissolved oxygen, suspended solids, chemical oxygen demand, nitrite, and labile phosphate as key environmental factors influencing the phytoplankton community structure (p < 0.05). In this study, the dynamic changes of phytoplankton community structure and environmental factors in the southern coastal waters of Beibu Gulf were analyzed in detail from two aspects of time and space. The key environmental factors to protect the ecological environment in the southern coastal area of Beibu Gulf were found out. It provides a reference method and theoretical basis for the management and protection of Beibu Gulf and other tropical marine environment.

Revealing microbial community characteristics in healthy human, cat and canine salivas and looking for species-specific microbes.

As two kinds of increasingly popular pets, the saliva of cat or canine is most likely to be left at the crime scene compared with the common types of body fluids in forensics. Accurately identifying the species of saliva samples found at the crime scene involving pets will help the investigators find available testing materials, reduce the consumption of reagents and save the investigative time of the case. Therefore, it is necessary to explore the characteristics and differences of saliva microbiomes of cat, canine and human. In this study, 16S rRNA gene amplicon sequencing technology was used to reveal microbial communities of saliva samples of healthy human, cat, and canine. Alpha diversity analyses indicated that canine saliva demonstrated the highest microbial diversity, followed by cat saliva, whereas human saliva microbial diversity was the lowest. The saliva samples of the three species all had their own unique microbial community compositions, and the dominant phyla of canine and cat salivas were Proteobacteria and Bacteroidete, while the dominant phyla of human saliva were Firmicutes and Proteobacteria. There was no significant statistical difference in the salivary microbiota obtained by the two collection methods (cotton swab and liquid saliva). The gender of cats and canines might have no effect on the salivary microbiota, but the different breeds had an impact on their saliva microbiomes. Principal coordinates analysis, non-metric multidimensional scaling analysis and random forest analysis all indicated significant differences in microbial community structures among the three species, allowing inference on the species sources of saliva samples by microbiome method. Differential microbial biomarkers for the salivas of three species were screened out using a variety of bioinformatics analyses, and the results demonstrated that Prevotella melaninogenica, Veillonella parvula, and Haemophilus parainfluenzae could be used as species-specific microbial biomarkers of human saliva. The detections of human species-specific microbes provide a potential method for determining human saliva.

Differences in Soil Fertility and Bacterial Community Structure Between Carbon Inputs such as Biochar and Organic Fertilizer and Their Relationship

The potato planting area of Guizhou Province ranks second in China. However, due to factors such as climatic conditions and unbalanced fertilization, soil organic matter in potato fields is consumed rapidly and has a large deficit, which affects soil biological function and soil fertility. Biochar and organic fertilizer are effective ways to supplement foreign aid organic matter to improve soil quality. However, the differences in soil fertility and microbial community structure and their relationships under the conditions of organic fertilizer or biochar combined with chemical fertilizer are not clear. In this study, three treatments of conventional fertilization （NPK）, increased application of biochar （NPKB）, and increased application of organic fertilizer （NPKO） were set up to investigate the characteristics of potato rhizosphere soil, bacterial community composition, and diversity； to analyze the effects of these factors on the soil integrated fertility index； and to explore the direct and indirect effects of IFI on soil fertility and bacterial community structure differences between treatments and their driving factors. The results showed that soil pH, available phosphorus （AP）, available potassium （AK）, total nitrogen （TN）, organic carbon （SOC）, and C/N ratio were significantly higher in the NPKB and NPKO treatments than in the NPK treatment （P<0.05）. Soil IFI was greatest for NPKO, followed by NPKB and least for the NPK treatment. A total of 8 214 ASVs were obtained from all the soil samples, belonging to 26 phyla, 75 classes, 165 orders, 176 families, and 251 genera （excluding unidentified fungi）. Proteobacteria, Actinobacteria, and Chloroflexi were the dominant phyla, accounting for 54.85% of all ASVs. Compared to that in the NPK and NPKB treatments, the NPKO treatment had the highest bacterial diversity and number of significantly different taxa, and soil AN, AP, AK, SOC, TN, and IFI were significant correlates of bacterial diversity index （P<0.05）. Additionally, pH, TN, and SOC were significant influencers of bacterial taxa differences （P<0.05）, with importance ranked as TN （70.59%） &gt; SOC （49.42%） &gt; pH （27.08%）. Structural equations suggested that pH-related soil properties and bacterial community diversity were the direct pathways influencing IFI, and soil pH-related soil characteristics could also indirectly affect IFI by affecting bacterial Shannon diversity. These results indicate that soil fertility and bacterial community structure were significantly different and correlated between the biochar and organic fertilizer addition treatments and that pH and bacterial community diversity were the key factors influencing IFI, with the NPKO treatment in particular having the best effect on improving IFI. Considering the effect of soil fertilization and the functional group of bacteria, NPKO is the recommended combination for the best synergistic effect of soil fertilization, that is, N 150 kg·hm-2+P2O5 135 kg·hm-2+K2O 135 kg·hm-2+organic fertilizer 6.6 t·hm-2.

Relationship between dynamic changes of microorganisms in Qupi and the quality formation of Fengxiangxing Huairang Daqu.

Fengxiangxing Huairang Daqu (FHD) is one of the major types of Daqu in China. However, the relationship between the microbial community structure at different stages, the changes in the sensory characteristics, fermentation characteristics, volatiles, the most critical process point, and the quality formation of FHD is not clear. Based on microscopic characterization, PacBio SMRT sequencing, and HS-SPME-GC-MS volatile metabolite analysis revealed the relationship between FHD quality formation and the dynamics of Qupi. The results showed that the 12th day of the culture was the most critical process point, highlighting the most significant differences in microbial community structure, sensory characteristics, fermentation characteristics, and flavor substances. Bacillus licheniformis (43.25%), Saccharopolyspora rectivirgula (35.05%), Thermoascus aurantiacus (76.51%), Aspergillus amstelodami (10.81%), and Saccharomycopsis fibuligera (8.88%) were the dominant species in FHD. S. fibuligera, A. amstelodami, and T. aurantiacus were associated with the snow-white color of the FHD epidermis, the yellow color of the interior, and the gray-white color, respectively. The abundance of T. aurantiacus, A. amstelodami, B. licheniformis, and S. rectivirgula was positively associated with the esterifying power and liquefying power of FHD. The abundance of T. aurantiacus and A. amstelodami was positively correlated with the saccharifying power of FHD. The abundance of S. fibuligera was positively related to the fermenting power of FHD. A total of 248 volatiles were detected in Qupi, mainly including alcohols, esters, aldehydes, and ketones. Of them, eleven volatiles had a significant effect on the flavor of Qupi, such as 1-butanol-3-methyl-, hydrazinecarboxamide, ethanol, phenylethyl alcohol, ethyl acetate, 2-octanone, 1-octen-3-ol, formic acid-hexyl ester, (E)-2-octen-1-ol, ethyl hexanoate, and 2(3H)-furanone-dihydro-5-pentyl-. The abundance of B. licheniformis, S. rectivirgula, T. aurantiacus, and S. fibuligera was positively correlated with the alcohols, aromatic compounds, and phenols in FHD. The abundance of S. fibuligera was positively correlated with the acids, esters, and hydrocarbons in FHD. These results indicate important theoretical basis and technical support for controllable adjustment of FHD microbial community structure, stable control of FHD quality, and precise, effective, and large-scale guidance of FHD production.

Similarities and differences in gastrointestinal microbiomes between wild and human-cared spotted dolphins (Stenella attenuata) in natural waters

Despite the growing awareness on the importance of gut microbiomes, understanding marine mammal gut microbiomes remains limited due to difficulties in sampling. Spotted dolphins (Stenella attenuata) are widely spread oceanic cetaceans, and there is a gap in knowledge regarding their gut microbiology. In this study, we opportunistically collected samples from both wild and human-cared spotted dolphins in the southern waters of Hainan Island, China. This provided the opportunity to examine the composition and diversity of the gut microbial communities of this cetacean species. Since these dolphins inhabit a similar water environment, different food sources might be the primary factor distinguishing the gut microbiomes of wild and human-cared populations, offering valuable experimental material to investigate potential differences in gut microbial community structure among marine mammals in similar environments but with varying food sources. We found that the gastrointestinal microbial community structure of wild and human-cared dolphins demonstrated significant differences, both overall and at specific locations. However, no significant difference was observed in the microbial diversity of their gastrointestinal tracts, indicating that the disparities primarily lie in microbiota composition. Additionally, we detected numerous potentially pathogenic bacteria, suggesting a comprehensive future study of marine mammal gut microbiology. Such a study might involve determining health indicator factors associated with these microbiomes. Our study not only supplements information on the gut microbiology of spotted dolphins but also delves into the similarities and differences in gastrointestinal microbial communities within the same marine mammal species when food source variations play a significant role in their lives.

Causes and consequences of microbiome formation in mosquito larvae

Abstract The assembly of host‐associated microbial communities is influenced by multiple factors, but the effect of microbiomes on host phenotypes is often not well understood. To address questions of food‐web effects on host microbiome assembly, we manipulated the resource environment (grass only [G] vs. grass + nutrients [GN]), competition type (intra‐ vs. inter‐specific) and density (high vs. low) for Culex restuans mosquito larvae. We predicted the microbial communities in fourth‐instar larvae would differ between these environmental treatments and that these treatments would translate into differences in the adult phenotype. Resource environment and density influenced the larval microbiome. In addition, the larval microbiome exhibited notable differences compared to the free‐living microbial communities. Resource‐driven differences in the larval samples can be attributed to Arcobacteraceae being more abundant in larvae reared in the GN treatments relative to those reared in the G treatments and Comamonadaceae being more abundant in the G treatment. Although significant, the difference in community structure between density treatments was difficult to discern. This appears to be driven by Weeksellaceae only being abundant in the high‐density, interspecific, GN treatment. Rearing larvae to adulthood under severe food limitation resulted in low survival (&lt;25%) in both resource environments. Approximately 60% of survivors to adulthood were male. Larvae reared in the intraspecific, G treatment had the shortest development time to adulthood and emerged as the smallest adults. These results demonstrate how environmental variation can significantly alter the alpha and beta diversity of free‐living microbes, which in turn can significantly affect host phenotype and critical life history traits, such as development time, size at adulthood, and survival. These findings highlight the importance of considering environmental influences on microbiome diversity to understand and predict host outcomes, offering valuable insights for diverse applications in fields such as ecology, public health, and agriculture.

Diversity and Isolation of Endophytic Fungi in Panax japonicus and Biotransformation Activity on Saponins.

This study reports the diversity and community structure differences of the endophytic fungi of Panax japonicus of different ages to obtain novel endophytic fungi with glycoside hydrolytic activity for rare saponins production. This study used the high-throughput sequencing method to analyze the diversity and community structure of endophytic fungi of P. japonicus. The endophytic fungi were processed by traditional isolation, culture, conservation, and ITS rDNA sequence analyses. Then the total saponins of P. japonicus were used as the substrate to evaluate the glycoside hydrolytic activity. The composition analysis of the community structure showed that the abundance, evenness, and diversity of endophytic fungi of nine-year-old P. japonicus were the best among all samples. A total of 210 endophytic fungi were isolated from P. japonicus samples and further annotated by sequencing the internal transcribed spacer. Then the biotransformation activity of obtained strains was further examined on total saponins of P. japonicus (TSPJ), with a strain identified as Fusarium equiseti (No.30) from 7-year-old P. japonicus showing significant glycoside hydrolytic activity on TSPJ, including ginsenoside Ro→zinglbroside R1, pseudoginsenoside RT1→pseudoginsenoside RP1, chikusetsusaponin IV→tarasaponin VI and chikusetsusaponin IVa →calenduloside E. These results reveal the diversity and community structure differences of the endophytic fungi of P. japonicus with different ages and establish a resource library of endophytic fungi of P. japonicus. More importantly, we identified a valuable endophytic fungus with glycoside hydrolytic activity and provided a promising convenient microbial transformation approach to produce minor deglycosylated ginsenosides.

Soil Fungal Community Differences in Manual Plantation Larch Forest and Natural Larch Forest in Northeast China.

Soil fungal communities are pivotal components in ecosystems and play an essential role in global biogeochemical cycles. In this study, we determined the fungal communities of a natural larch forest and a manual plantation larch forest in Heilongjiang Zhongyangzhan Black-billed Capercaillie Nature Reserve and Gala Mountain Forest using high-throughput sequencing. The interactions between soil fungal communities were analysed utilising a co-occurrence network. The relationship between soil nutrients and soil fungal communities was determined with the help of Mantel analysis and a correlation heatmap. The Kruskal-Wallis test indicated that different genera of fungi differed in the two forest types. The results show that there was a significant change in the alpha diversity of soil fungal communities in both forests. In contrast, nonmetric multidimensional scaling (NMDS) analysis showed significant differences in the soil fungal community structures between the manual plantation larch forest and the natural larch forest. The soil fungal co-occurrence network showed that the complexity of the soil fungal communities in the manual plantation larch forest decreased significantly compared to those in the natural larch forest. A Mantel analysis revealed a correlation between the soil fungal co-occurrence network, the composition of soil fungi, and soil nutrients. The RDA analysis also showed that AN, TK, and pH mainly influenced the soil fungal community. The null model test results showed the importance of stochastic processes in soil fungal community assembly in manual plantation larch forests. Overall, this study enhances our understanding of the differences in soil fungal communities in manual plantation larch forests and natural larch forests, providing insights into their sustainable management. It also serves as a reminder that the ecological balance of natural ecosystems is difficult to restore through human intervention, so we need to protect natural ecosystems.

Biodiversity of Nematodes from Coral Reef Sediments in the South China Sea Based on eDNA Metabarcoding

Coral reef ecosystems in the South China Sea are one of the globally important marine biodiversity hotspots. However, there are few studies on nematode biodiversity in coral reef sediments. Here, we assessed nematode biodiversity in coral reef sediments in the South China Sea using eDNA metabarcoding. Eight sampling stations were set up in the region north of the South China Sea Basin (Xisha and Zhongsha Islands) and south of it (Nansha Islands), respectively. We also compared and analysed the nematode biodiversity and community structure in different regions, as well as the effects of environmental factors on the community structure. The results showed that a total of 503 operational taxonomic units (OTUs) were detected in 16 sediment samples. The nematodes identified belong to two classes, 10 orders, 37 families, 51 genera and 61 species, and all of them were Enoplea and Chromadorea, except for the unidentified taxa, which accounted for 97.26% of the total abundance. The analyses showed that the northern region had higher nematode abundance and diversity relative to the southern region. However, there was no significant difference in the nematode community structure between the two regions, which was less affected by geographic location. Similarly, environmental factors (total nitrogen, total phosphorus, copper, zinc, cadmium, lead and arsenic) have an effect on the abundance of specific nematode groups but not on the overall community structure. In summary, this study initially reveals the composition and diversity of nematode communities in coral reef sediments in the South China Sea and provides an important reference for further in-depth study of the South China Sea ecosystem.

Comparison of microbial diversity and metabolic activities in organic and conventional rice farms in Thailand.

Studies of the soil microbial community have revealed that several factors, both biotic and abiotic, can influence the community structure, diversity, and function. Human agricultural practice has been one of the key factors that affect microbial structure in soil. In this study, we examined the effect of two rice farming practices (i.e., conventional and organic) on soil microbial diversity and their metabolic activities. We proposed that the use of herbicides and chemical fertilizers in the conventional rice farming may decrease the soil microbial diversity and that it may lead to a decline in soil quality. However, our results show that there is no significant difference in the soil chemical properties, microbial diversity, and microbial metabolic activities between the two agricultural management systems. The wetland water cycling regime of rice agriculture in Thailand perhaps prevents the accumulation of chemicals in the soil, thus subdue the effect of these chemicals on soil microbes. Furthermore, our results showed that the key determinant of soil chemical properties as well as microbial community structure and diversity is the soil physical property, while the farming activity influences the microbial metabolic functions. These findings indicate the complex nature of the soil, microbes, and human farming interactions.IMPORTANCERice is a major export commodity in Thailand. As such, an understanding of the effect of conventional or organic farming approaches on soil microbial community could enable a suitable farming management. In this study, microbial communities were surveyed and compared between the two rice farming practices for their diversity and metabolic activities. Results showed no significant differences in microbial community structure and diversity between the two rice farming practices, but significant differences were observed due to the soil type, namely, clay, silty clay, silty clay loam, loam, and silty loam. Interestingly, significant differences in metabolic functions were also observed in different soil farming activities, such as land rest, period of growth, and post-burning, but not due to conventional or organic practices. These findings showed that the soil physical type and the farming activity impact the microbial community more than whether it is conventional or organically farmed.

Leaf Health Status Regulates Endophytic Microbial Community Structure, Network Complexity, and Assembly Processes in the Leaves of the Rare and Endangered Plant Species Abies fanjingshanensis.

The rare and endangered plant species Abies fanjingshanensis, which has a limited habitat, a limited distribution area, and a small population, is under severe threat, particularly due to poor leaf health. The plant endophytic microbiome is an integral part of the host, and increasing evidence indicates that the interplay between plants and endophytic microbes is a key determinant for sustaining plant fitness. However, little attention has been given to the differences in the endophytic microbial community structure, network complexity, and assembly processes in leaves with different leaf health statuses. Here, we investigated the endophytic bacterial and fungal communities in healthy leaves (HLs) and non-healthy leaves (NLs) of A. fanjingshanensis using 16S rRNA gene and internal transcribed spacer sequencing and evaluated how leaf health status affects the co-occurrence patterns and assembly processes of leaf endophytic microbial communities based on the co-occurrence networks, the niche breadth index, a neutral community model, and C-score metrics. HLs had significantly greater endophytic bacterial and fungal abundance and diversity than NLs, and there were significant differences in the endophytic microbial communities between HLs and NLs. Leaf-health-sensitive endophytic microbes were taxonomically diverse and were mainly grouped into four ecological clusters according to leaf health status. Poor leaf health reduced the complexity of the endophytic bacterial and fungal community networks, as reflected by a decrease in network nodes and edges and an increase in degrees of betweenness and assortativity. The stochastic processes of endophytic bacterial and fungal community assembly were weakened, and the deterministic processes became more important with declining leaf health. These results have important implications for understanding the ecological patterns and interactions of endophytic microbial communities in response to changing leaf health status and provide opportunities for further studies on exploiting plant endophytic microbes to conserve this endangered Abies species.

Archaeal communities in natural and artificially restored mangrove sediments in Tieshan Bay, China

Mangrove forests are crucial wetland ecosystems located in tropical and subtropical intertidal zones, but they have become extensively degraded. As a viable ecological restoration strategy, the cultivation of native mangrove vegetation in these degraded areas has gained considerable attention. Mangroves’ unique environmental conditions make them suitable habitats for diverse microbial communities, including Archaea - one of the main microbial communities in mangrove sediments - which plays a pivotal role in biogeochemical cycles. However, little is known about the dynamics of archaeal communities during mangrove restoration through phytoremediation. In this study, we investigated the physicochemical properties of sediment profiles from natural and artificially restored mangrove ecosystems in Tieshan Bay. We utilized quantitative polymerase chain reaction (qPCR) and 16S rRNA gene sequencing techniques to explore differences in abundance, community structure, and composition of archaeal communities between sediment profiles in natural and artificially restored mangrove ecosystems. We also examined correlations between archaeal communities and environmental factors. Our results revealed that Crenarchaeota, Thermoplasmatota, Asgardarchaeota, Nanoarchaeota, and Euryarchaeota were the predominant archaeal phyla, with significant variation in sediment composition observed for Crenarchaeota and Thermoplasmatota in different depths. We also found significant differences in archaeal abundance and community composition between natural and restored mangrove sediments. Furthermore, C/N ratio and pH emerged as primary drivers of archaeal communities in wet and dry season sediments, respectively. Additionally, the study revealed seasonal disparities in seasonal differences in the relative abundance of certain archaeal groups (such as Asgardarchaeota, Nanoarchaeota). Network analysis demonstrated stronger interconnections among archaeal communities in sediments from natural mangroves than from artificially restored ones. These findings enhance our knowledge of archaeal community succession patterns in mangrove restoration, as well as provide fresh perspectives for the sustainable management of mangrove ecosystems.

BIODIVERSITAS GASTROPODA DI HUTAN MANGROVE SEGARA ANAKAN CILACAP

Segara Anakan is a lagoon surrounded by swamp forest with a mud substrate. Several biota live in it, one of which is Gastropods. This biota has slow movements and is relatively sedentary. The aim of research on gastropod biodiversity is to describe the diversity and dominance of their species. The research was conducted in July-September 2021. The research method used was a survey with a purposive random sampling technique at three stations taking into account differences in vegetation community structure. Station 1 (St 1) is in the eastern part of Segara Anakan with vegetation that dominates Aegiceras corniculatum; Station 2 (St 2) is in the middle of Segara Anakan with vegetation that dominates Nypa fruticans; Station 3 (St 3) is in the western part of Segara Anakan with vegetation dominating Sonneratia alba. Each station is determined by nine different sampling points once every month. The results showed that the Potamididae and Neritidae families were most commonly found at all stations during the study. The highest abundance is found in St 3, namely 1433 ind/m2, the lowest in St 1, namely 545 ind/m2. The diversity index in the medium category is at St 1 (1.05) and St 3 (1.59), while the low category is at St 2 (0.85). The dominance index in the medium category is at St 2 (0.55), and in the low category at St 1 (0.47) and St 3 (0.28). Factors that influence differences in abundance, diversity and dominance are adaptation, food and environmental conditions in which they live.

Particle size shapes prokaryotic communities and vertical connectivity in the water columns of the slope and central basin of the South China Sea

Sinking of organic matter represents an essential mechanism for sequestration of carbon that is exported from the ocean surface to deeper depths. While recent studies have highlighted the important role of microorganisms in the biological pump, the impact of sinking particles on the vertical connectivity of microbial communities has received limited attention. In this study, we present the microbial profile of sinking particles in the northern slope and the central basin of the marginal South China Sea (SCS) using an in-line size-fractionated water filtration and Illumina high-throughput 16S rRNA amplicon sequencing. We investigate the microbial community composition within organic particles of different size fractions (30, 5, 3, 0.22 μm), and we reveal significant differences in the microbial community structure between these two distinct areas of SCS. The vertical connectivity of microbial communities in the slope and the central basin of SCS shows distinct patterns of microbial dispersal along the water column that occurs via the sinking of organic particles. We find that the microbial communities have different abundances on the different examined particle size fractions and which highlights the role of sinking particles in shaping microbial lifestyles along the water column. Our study underscores the influence of environmental variations on the vertical connectivity of microorganisms and provides additional insights into the marine biological pump under different environmental conditions.

PhoD-harboring bacterial community assembly and co-occurrence in soil aggregates during roadside slope restoration

Soil organic phosphorus (OP) mineralization plays a vital role in the ecological restoration of roadside slopes. However, the changes in the functional bacterial (phoD-harboring) community involved in OP mineralization in soil aggregates during slope restoration are still unknown. In this study, a space-for-time substitution was conducted to compare the differences in the phoD-harboring bacterial community structure and assembly in soil aggregates of four particle sizes (<0.053, 0.25–2, 0.053–0.25, and >2 mm) at different slope restoration ages (7, 11, and 14 years). The results showed no significant differences in the phoD-harboring community diversity and structure among soil aggregates in the same restoration year. Community structure dissimilarity increased with restoration time. Species replacement dominated slope soils restored for 7, 11, and 14 years, accounting for 78.40 %, 79.68 %, and 68.96 % of the total β-diversity, respectively. Community assembly processes shifted from coexisting deterministic (68 %) and stochastic (32 %) processes in the 7-year restoration slope soil to dominantly deterministic (98 % and 91 %) processes in the 11- and 14-year restoration slope soils, respectively. Dominant phoD-harboring bacteria tended to shift from r-to K-strategies as slope restoration progressed, and the C:P ratio significantly correlated with both community structure and assembly. The increasing C:P ratio over restoration time stimulated phoD-harboring bacteria to secrete alkaline phosphatase to improve P availability, enhancing the complexity and stability of the network. This study elucidates the changing patterns of phoD-harboring bacteria in soil aggregates and provides a theoretical basis for the management of soil P during roadside restoration.

Thermal tolerance as a driver of reef fish community structure at the isolated tropical Mid-Atlantic Ridge Islands

Reef fish communities are shaped by historical and ecological factors, including abiotic and biotic mechanisms at different spatial scales, determining species composition, abundance and biomass. The oceanic islands in the Mid-Atlantic Ridge (St. Peter and St. Paul's Archipelago - SPSPA, Ascension, and St. Helena), exhibiting differences in community structure along a 14-degree latitudinal and a 10 °C thermal gradient. We investigate the influence of sea surface temperature, area, age, isolation and phosphate on reef fish community structures. Reef fish trophic structure varies significantly across the islands, with planktivores and herbivore-detritivores showing the highest abundances in SPSPA and Ascension, while less abundant in St. Helena, aligning with the thermal gradient. Variations in reef fish community structures were predominantly influenced by thermal regimes, corroborating the expansion of species' thermal niche breadth at higher latitudes and lower temperatures. This study highlights that in addition to biogeographic factors, temperature is pivotal on shaping oceanic island reef fish community structure.

Ecological status of a retired mine lake in a protected dune ecosystem

ABSTRACT Ottawa Sands Lake is a retired mine lake located in a protected dune ecosystem adjacent to Lake Michigan in western Michigan, USA. Development activities are planned for the lake and surrounding land, potentially threatening the lake’s ecological health. We conducted a baseline study of water quality and macroinvertebrates, combined with exclusion cage experiments, to examine the role of predation. Our results indicated the lake’s littoral zone had good water quality with low phosphorus (mean soluble reactive phosphorus [SRP] < 5 µg/L; mean total phosphorus [TP] < 10 µg/L) and nitrogen (mean nitrate [NO3-N] = 38–190 µg/L; mean ammonia [NH3-N] = 8–19 µg/L, excluding deep hole) concentrations, high dissolved oxygen (>9.5 mg/L, excluding deep hole), and low chlorophyll a (<12 µg/L, except for 1 sampling date) concentrations. The macroinvertebrate community was dominated by 9 families, with Chironomidae the most abundant. Three environmental factors—specific conductivity, total dissolved solids, and ammonia—were significantly related, albeit weakly, to macroinvertebrate community structure. The exclusion cages did not result in a statistically significant difference in macroinvertebrate community structure, although high variance may have masked differences. Overall, Ottawa Sands Lake is a high-quality system, but development plans, including the installation of a paved trail around the lake and the implementation of a nonmotorized boating program, may result in changes. The baseline conditions outlined in this work will allow lake managers to assess the impact of development activity and add to the limited database regarding the limnology of retired mine lakes around the globe.

Variation in soil bacterial community characteristics inside and outside the West Ordos National Nature Reserve, northern China.

Nature reserves are crucial for protecting biological habitats and maintaining biodiversity. Soil bacterial community plays an irreplaceable role in the structure and function of ecosystem. However, the impact of nature reserves on soil bacterial communities is still unclear. To explore the effects of desert grassland nature reserve management on soil microbial communities, we compared the differences in soil bacterial community composition, α-diversity and community structure inside and outside a desert grassland nature reserve, and explored the correlation between soil bacterial communities and plant biomass and soil chemical index. We found that (1) the relative abundance of Acidobacteriota is highest in the soil both inside and outside the nature reserve in shrub grassland; (2) the Chao1 index of soil bacterial communities in the core protected zone and general control zone of the reserve was significantly higher than that outside the reserve (p < 0.05) in the shrub grassland. Similarly, in the herbaceous grassland, the Shannon index of soil bacterial communities was significantly higher in the core protected zone of the reserve than that outside the reserve (p < 0.05). (3) While we found no significant difference in soil bacterial community structure between inside and outside the reserve in the shrub grassland, we found that the soil bacterial community structure in the core protected zone was significantly different from that outside the reserve in the herbaceous grassland (p < 0.05); (4) we also found that higher plant productivity and soil nutrients promoted most soil dominant bacterial phyla, while higher soil pH and salinity inhibited most soil dominant bacterial phyla. Our findings thus help better understand the influencing factors of and the mechanisms behind variation in soil bacterial communities inside and outside desert grassland nature reserves.

Withdrawn: The altered dynamic community structure for adaptive adjustment in stroke patients with multidomain cognitive impairments: A multilayer network analysis

BackgroundInternal capsule strokes can lead to multidomain cognitive impairments, and while the brain showcases adaptability post-stroke, the interplay between this adaptability and multidomain cognitive function remains elusive. In addition, although most studies indicate that adaptive changes after stroke manifest as brain functional network abnormalities, the changes in dynamic topological features, especially dynamic community structure, required for adaptive adjustment in stroke patients are not yet clear. MethodsResting-state fMRI data were acquired from patients with infarct in left-sided (n = 46, CI_L) and right-sided (n = 45, CI_R) internal capsule and 81 healthy controls (HC). Dynamic network matrices were generated using a sliding-window approach. These matrices were partitioned into communities utilizing a multilayer community detection algorithm. The network switching rate were employed as a key metric to characterize the differences of dynamic community structure between stroke and HC groups, and the correlations between these significant intergroup differences and cognitive performance scores was calculated. ResultsCompared to HC, CI_L patients exhibited an increase in network switching rates across all networks in the whole brain. However, these increases were largely unbeneficial for cognitive recovery; CI_R group show a more limited range of increased network switching rates and a more limited negative correlations with cognitive performance. ConclusionsThis study elucidates that following a stroke, the brain continuously adapts its dynamic community structure in an effort to address multidomain cognitive impairments, but this adaptation is often ineffective, unorganized, and disordered. Moreover, these findings elucidate the lateralized effects of stroke lesions on dynamic reorganization.