Differences In Community Composition Research Articles

Differences in bacterial community composition between fish-stocked and fishless lakes from an arid Patagonian plateau

Differences in bacterial community composition between fish-stocked and fishless lakes from an arid Patagonian plateau

Impacts of anthropogenic habitat modification on mammalian diversity in the Mau Forest Complex, Kenya

Habitat destruction is a major driver of biodiversity loss, especially in the tropics. We investigated changes in the diversity and occupancy of forest-dwelling mammals in response to habitat loss, alteration, and degradation at the Mau Forest Complex (MFC), southwestern Kenya. Using a systematic camera trapping grid, we estimated patterns of mammalian diversity, occupancy of small carnivores, and detection rates of functional mammalian groups across three habitat types (primary forests, secondary forests, and cultivated habitats). Between March 2019 and October 2021, 246 camera traps were deployed across 181 locations representing 5,509 sampling days, resulting in 47,345 images of 52 mammalian species in nine mammalian orders. Alpha diversity differed among treatments, with primary forests having the highest diversity, and cultivated habitats the lowest, though results were not statistically significant. Beta diversity differed significantly among treatments, indicating differences in community composition as well as species richness. Overall occupancy for small carnivores was highest in primary forests and lowest in cultivated habitats, with some species specializing in primary forests while others were able to occupy more degraded habitats. Among functional groups, detection rates only differed significantly for large rodents, primates, and ungulates. Our results indicate that although functional groups and species may respond differently to habitat loss and alteration at the MFC, overall species diversity of specialist mammals was highest in the less-disturbed primary forests. Specialist, forest-dependent species are likely most affected by human activities, making them especially vulnerable to habitat loss at the MFC.

Drought mediates the response of soil fungal communities post-wildfire in a Californian grassland and coastal sage scrubland

There is a knowledge gap surrounding how drought and wildfire, two increasingly frequent disturbances, will alter soil fungal communities. Moreover, studies that directly compare ambient and drought-treated soil fungal communities in the context of wildfire are exceptionally scarce. We assessed the response and recovery of soil fungal communities and functional guilds in two sites – a grassland and a coastal sage shrubland – after a severe wildfire burned a long-term drought experiment. We collected soil samples at four collection dates over an eight-month period after wildfire and amplified fungal DNA. We predicted that fungal communities within the drought and ambient treatments would differ significantly across collection dates owing to differing responses to post-wildfire conditions. Richness was stable across collection dates, regardless of precipitation treatment, in both sites. Differences between treatments were significant at every collection date with respect to taxonomical community composition. Differences in community composition between collection dates within each treatment were also significant. Additionally, the monotonic trends of drought and ambient communities over time differed in strength and direction. Differences in shrubland functional guild composition across collection dates and contrasting trends suggest a drought-dependent shift after the fire. Overall, we conclude that drought mediates how soil fungal communities respond after a wildfire in the long term, however drought effects may differ across ecosystems.

Effects of coagulation pre-treatment on chemical and microbial properties of water-soil-plant systems of constructed wetlands

Chemical coagulation has gained recognition as an effective technique to enhance the removal efficiency of pollutants in wastewater prior to their entry into a constructed wetland (CW) system. However, its potential impact on the chemical and microbial properties of soil and plant systems within CWs requires further research. This study investigated the impact of using ferric chloride (FeCl3) as a pre-treatment stage for dairy wastewater (DWW) on the chemical and microbial properties of water-soil-plant systems of replicated pilot-scale CWs, comparing them to CWs treating untreated DWW. CWs treating amended DWW had better performance than CWs treating raw DWW for all water quality parameters (COD, TSS, TP, and TN), ensuring compliance with the EU wastewater discharge directives. Soil properties remained mostly unaffected except for pH, calcium and phosphorus (P), which were lower in CWs treating amended DWW. As a result of lower nitrogen (N) and P loads, the plants in CWs receiving FeCl3-amended DWW had lower N and P contents than the plants of raw DWW CWs. However, the lower loads of P into amended DWW CWs did not limit the growth of Phragmites australis, which were able to accumulate trace elements higher than CWs receiving raw DWW. Alpha and Beta-diversity analysis revealed minor differences in community richness and composition between both treatments, with only 3.7% (34 genera) showed significant disparities. Overall, the application of chemical coagulation produced superior effluent quality without affecting the properties of soil and plant of CWs or altering the functioning of the microbial community.

Composition and distribution of bacterial communities and potential radiation-resistant bacteria at different elevations in the eastern Pamirs.

Altitude and ultraviolet (UV) radiation may affect the community composition and distribution of microorganisms in soil ecosystems. In this study, 49 soil samples from 10 locations were collected from different elevations on the eastern Pamir Plateau and analyzed for soil microbial community structure and function using high-throughput sequencing. The results showed that soil samples from different elevations of the eastern Pamir Plateau contained 6834 OTUs in 26 phyla and 399 genera. The dominant phyla common to different elevations were Actinobacteria, Proteobacteria, Bacteroidota, Acidobacteriota, and Gemmatimonadota. The dominant genera were Rubrobacter, Sphingomonas, Nocardioides, and Solirubrobacter. Species richness increased slightly with elevation, and there were significant differences in community composition between the elevations. Elevation and UV exposure are important factors that drive changes in bacterial communities. The results of the KEGG pathway showed that drug resistance, antineoplastic, aging, replication, and repair were enhanced and then slightly decreased with increasing elevation. Bacterial communities at different elevations were rich in radiation-resistant microorganisms, and the main genera were Rubrobacter, Sphingomonas, Nocardioides, Pontibacter, and Streptomyces. The findings have shown the composition and distribution of bacterial communities at different elevations on the Eastern Pamir Plateau. Potentially radiation tolerant microbial species were also examined. The results are of considerable importance for the succession of bacterial microorganisms in the plateau region, the study of radiation tolerant bacterial germplasm resources, and the application of biofunctionality.

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.

Legacy copper/nickel mine tailings potentially harbor novel iron/sulfur cycling microorganisms within highly variable communities.

The oxidation of sulfide-bearing mine tailings catalyzed by acidophilic iron and sulfur-oxidizing bacteria releases toxic metals and other contaminants into soil and groundwater as acid mine drainage. Understanding the environmental variables that control the community structure and metabolic activity of microbes indigenous to tailings (especially the abiotic stressors of low pH and high dissolved metal content) is crucial to developing sustainable bioremediation strategies. We determined the microbial community composition along two continuous vertical gradients of Cu/Ni mine tailings at each of two tailings impoundments near Sudbury, Ontario. 16S rRNA amplicon data showed high variability in community diversity and composition between locations, as well as at different depths within each location. A temporal comparison for one tailings location showed low fluctuation in microbial communities across 2 years. Differences in community composition correlated most strongly with pore-water pH, Eh, alkalinity, salinity, and the concentration of several dissolved metals (including iron, but not copper or nickel). The relative abundances of individual genera differed in their degrees of correlation with geochemical factors. Several abundant lineages present at these locations have not previously been associated with mine tailings environments, including novel species predicted to be involved in iron and sulfur cycling.IMPORTANCEMine tailings represent a significant threat to North American freshwater, with legacy tailings areas generating acid mine drainage (AMD) that contaminates rivers, lakes, and aquifers. Microbial activity accelerates AMD formation through oxidative metabolic processes but may also ameliorate acidic tailings by promoting secondary mineral precipitation and immobilizing dissolved metals. Tailings exhibit high geochemical variation within and between mine sites and may harbor many novel extremophiles adapted to high concentrations of toxic metals. Characterizing the unique microbiomes associated with tailing environments is key to identifying consortia that may be used as the foundation for innovative mine-waste bioremediation strategies. We provide an in-depth analysis of microbial diversity at four copper/nickel mine tailings impoundments, describe how communities (and individual lineages) differ based on geochemical gradients, predict organisms involved in AMD transformations, and identify taxonomically novel groups present that have not previously been observed in mine tailings.

Determining the footprint of breeding in the seed microbiome of a perennial cereal

BackgroundSeed endophytes have a significant impact on plant health and fitness. They can be inherited and passed on to the next plant generation. However, the impact of breeding on their composition in seeds is less understood. Here, we studied the indigenous seed microbiome of a recently domesticated perennial grain crop (Intermediate wheatgrass, Thinopyrum intermedium L.) that promises great potential for harnessing microorganisms to enhance crop performance by a multiphasic approach, including amplicon and strain libraries, as well as molecular and physiological assays.ResultsIntermediate wheatgrass seeds harvested from four field sites in Europe over three consecutive years were dominated by Proteobacteria (88%), followed by Firmicutes (10%). Pantoea was the most abundant genus and Pantoea agglomerans was identified as the only core taxon present in all samples. While bacterial diversity and species richness were similar across all accessions, the relative abundance varied especially in terms of low abundant and rare taxa. Seeds from four different breeding cycles (TLI C3, C5, C704, C801) showed significant differences in bacterial community composition and abundance. We found a decrease in the relative abundance of the functional genes nirK and nifH as well as a drop in bacterial diversity and richness. This was associated with a loss of amplicon sequence variants (ASVs) in Actinobacteria, Alphaproteobacteria, and Bacilli, which could be partially compensated in offspring seeds, which have been cultivated at a new site. Interestingly, only a subset assigned to potentially beneficial bacteria, e.g. Pantoea, Kosakonia, and Pseudomonas, was transmitted to the next plant generation or shared with offspring seeds.ConclusionOverall, this study advances our understanding of the assembly and transmission of endophytic seed microorganisms in perennial intermediate wheatgrass and highlights the importance of considering the plant microbiome in future breeding programs.

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.

Gut microbial signatures of patients with diarrhea-predominant irritable bowel syndrome and their healthy relatives

Abstract Aims Irritable bowel syndrome (IBS) is a prevalent gastrointestinal disorder, encompassing diarrhea-predominant irritable bowel syndrome (IBS-D). Here, we utilized 16S rDNA gene sequencing to identify potential microbial drivers of IBS-D. Methods and Results A total of 30 healthy relatives and 27 patients with IBS-D were recruited. Clinical data and fecal samples were collected from patients and controls. 16S rDNA gene sequencing was performed to obtain fecal bacterial data. Differences in community composition were evaluated utilizing analysis of similarity (ANOSIM) using Bray–Curtis dissimilarity. The Wilcoxon rank sum test was used to compare differences in taxa and functional pathways. Finally, the key gut microbiota was identified using the random forest algorithm. Gut microbiota diversity, estimated through the Observe, Chao1, and abundance-based coverage estimator (ACE) indices, was significantly lower in the IBS-D patients than in the healthy relatives. ANOSIM analysis further confirmed significant differences in the composition of the gut microbiota between IBS-D patients and healthy relatives, with an R value of 0.106 and a P-value of 0.005. Notably, the IBS-D patients exhibited a significant enrichment of specific bacterial genera, including Fusicatenibacter, Streptococcus, and Klebsiella, which may possess potential pathogenic properties. In particular, the bacterial genus Klebsiella demonstrated a positive correlation with irritable bowel syndrome severity scoring system scores. Conversely, healthy subjects showed enrichment of bacterial genera such as Alistipes, Akkermansia, and Dialister, which may be beneficial bacteria in IBS-D. Utilizing the random forest model, we developed a discriminative model for IBS-D based on differential bacterial genera. This model exhibited impressive performance, with an area under the curve value of 0.90. Additionally, our analysis did not reveal any gender-specific differences in the microbiota community composition among IBS-D patients. Conclusions Our findings offer preliminary insights into the potential relationship between intestinal microbiota and IBS-D. The identification model for IBS-D, grounded in gut microbiota, holds promising prospects for improving early diagnosis of IBS-D.

Long-term subsoiling and tillage rotation increase carbon storage in soil aggregates and the abundance of autotrophs

Autotrophic microorganisms in soil can increase soil carbon (C) sequestration by utilising chemical energy released from inorganic compounds to fix atmospheric CO2. Therefore, the effects of tillage systems on soil C stocks and autotrophic microbial community deserves in-depth study. The effects of five tillage systems, including no tillage (NoTill), subsoiling (SubS), rotary tillage (RotTill, local general tillage), no tillage-subsoiling-no tillage (NoTill-SubS), and rotary tillage-subsoiling-rotary tillage (RotTill-SubS) were investigated within a 17-year field experiment. Their effects on soil aggregates, C content and enzyme activities were studied, and the impacts on C-fixing microbial communities were analysed using the C-fixing gene cbbL. The macroaggregate portion and RubisCO and ATPase activities were the highest under SubS, causing the aggregate-associated organic C (AOC) to be 93 % higher than that under RotTill. Under RotTill-SubS, SOC, AOC and aggregate-associated microbial biomass C (AMBC) were larger than those under RotTill. RotTill-SubS reduced the microaggregate portion, increased enzyme activities and the relative abundance of C-fixing bacteria, including Sphingomonadales, Burkholderiales, and Nitrosomonadales. The macroaggregate portion under NoTill-SubS and the relative abundance of Sphingomonadales and Burkholderiales was the highest. Correspondingly, the SOC content was the largest (29 % higher than that in RotTill), and the AOC and AMBC contents were 42 % and 31 % larger, respectively, than those in RotTill. Structural equation modelling reveals that increasing tillage or lowering AOC content can directly increase differences in autotrophic bacterial communities. The reduced aggregate stability decreases C content and increases ATPase and RubisCO activities can indirectly increase differences in bacterial community composition.

Response of Microbial Communities to Naturally Occurring Radioactive Material-Contaminated Sediments: A Microcosm-Based Study.

There is a growing need to understand the potential ecological impacts of contaminants in offshore oil and gas infrastructure, especially if that infrastructure is to be left in situ as a decommissioning option. Naturally occurring radioactive material (NORM) is one type of contaminant found in solid deposits on internal surfaces of infrastructure that poses potential ecological harm if released into the marine environment. Microbes are important components of marine sediment ecosystems because they provide ecosystem services, yet the impacts of NORM contamination to these communities are not well understood. The present study aimed to investigate the response of benthic microbial communities to NORM-contaminated scale, collected from an offshore oil and gas system, via controlled laboratory microcosm studies. Changes to microbial communities in natural sediment and sediments spiked with NORM at radium-226 activity concentrations ranging from 9.5 to 59.8 Bq/kg (in partial equilibria with progeny) over 7 and 28 days were investigated using high-throughput sequencing of environmental DNA extracted from experimental sediments. There were no significant differences in microbial community composition between control and scale-spiked sediments over 7 and 28 days. However, we observed a greater presence of Firmicutes in the scale-mixed treatment and Chloroflexi in the scale-surface treatments after 28 days. This could suggest selection for species with contaminant tolerance or potential resilience to radiation and metal toxicity. Further research is needed to explore microbial tolerance mechanisms and their potential as indicators of effects of radionuclide-contaminated sediments. The present study demonstrated that microcosm studies can provide valuable insights about the potential impacts of contamination from oil and gas infrastructure to sediment microbial communities. Environ Toxicol Chem 2024;43:1648-1661. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Rainforest transformation reduces parasitoid wasp diversity—Can the enrichment of flowering vegetation alleviate this?

Abstract In Indonesia, the rapid expansion of oil palm and rubber plantations replaces large areas of tropical rainforest. Rainforest transformation alters the diversity and composition of parasitoid wasp communities, but appropriate management strategies to buffer their decline in rainforest transformation landscapes are not yet developed. Here, we studied the effects of rainforest conversion to smallholder rubber and oil palm plantations on parasitoid wasp species richness, abundance and species composition. We also conducted a flowering vegetation enrichment experiment using the flowering weed Asystasia gangetica in all land‐uses to investigate potential mitigation effects on parasitoid wasp diversity and composition. Rainforest transformation to rubber plantations caused a large decrease in species richness (46%) and abundance (59%) of parasitoid wasps. Community structure of parasitoid wasps differed between forest and monoculture habitats with more habitat‐specialised species in forest and a higher proportion of common species in the monoculture. The experimental flowering vegetation enrichment increased parasitoid wasp species richness by 18% and abundance by 127%. Enrichment also enhanced the presence of unique parasitoid species in plantation and furthermore increased differences in community composition between rainforest and plantations. However, the enrichment experiment was confounded by time, meaning that a multi‐year experiment with targeted controls is necessary for statistically more reliable statements. Our study shows the effect of rainforest transformation to oil palm and rubber plantations on parasitoid wasp communities. Although providing additional flowering vegetation in plantations seems to potentially mitigate diversity loss, further research is needed to confirm and to investigate the mechanisms how flowering plants alleviate negative effects of rainforest transformation on parasitoid communities. Thereby, efficient conservation strategies for parasitoids wasps and their biological control services can be developed for rapidly changing tropical landscapes.

Unveiling soil bacterial ecosystems in andean citrus orchards of Santander, Colombia

Citrus cultivation is vital to global agriculture, necessitating a comprehensive understanding of the soil microbiome’s diversity for sustainable practices. This study provides initial insights into the bacteriome in citrus crops in Santander, Colombia, employing a holistic approach combining culture-based techniques, sequencing methods, and bioinformatics analyses. The study explores organic and non-organic cultivation systems, revealing statistically significant differences in bacterial community composition between both practices. In general, the communities are dominated by members of the Actinobacteria and Proteobacteria, along with bacterial orders Gaiellales and Burkholderiales, all contributing to intricate ecological processes. Culture-based methods aided in the isolation of potential biotechnologically relevant strains. Among them, strain CP102 showed a pronounced carboxymethylcellulose (CMC) degradation capacity. Genetic analysis of the isolate resulted in the generation of the first closed genome of a member of the species Enterobacter soli and identified an unreported 109 kb plasmid. Further genomic examination revealed genes potentially associated with cellulose degradation in this species, which provides the isolate with biotechnological potential. This research significantly advances the global understanding of citrus-associated bacteriomes, shaping future agricultural practices and promoting the development of sustainable bioproducts.

Comprehensive analysis of the gut microbiota in patients with chronic obstructive pulmonary disease of varying severity-A prospective, observational study

Accumulating evidence has highlighted the influence of the gut microbiota on lung immunity. We examined the effects of changes in intestinal microecology on the development of Chronic Obstructive Pulmonary Disease (COPD) and identified microbial biomarkers for acute exacerbations of COPD (AECOPD). Fecal samples were collected from 30 patients with stable COPD, 30 patients with AECOPD, and 10 healthy individuals. Fecal microbiological profiles were analyzed using 16S rRNA gene sequencing. The results showed a distinct difference in the bacterial community composition between the AECOPD, COPD, and healthy control groups. The COPD and AECOPD groups had higher levels of Firmicutes but lower levels of Bacteroidetes compared to the healthy control group at the phylum level. At the genus level, there was an increased abundance of Lachnoclostridium, Alistipes, Streptococcus, and Prevotella in COPD and AECOPD patients. Increasing levels of Lachnoclostridium and Prevotella may indicate an acute exacerbation of COPD. This study identified specific microbial biomarkers associated with AECOPD and characterized the composition of gut microbiota in patients with AECOPD.

Biochar is colonized by select arbuscular mycorrhizal fungi in agricultural soils

Arbuscular mycorrhizal fungi (AMF) colonize biochar in soils, yet the processes governing their colonization and growth in biochar are not well characterized. Biochar amendment improves soil health by increasing soil carbon, decreasing bulk density, and improving soil water retention, all of which can increase yield and alleviate environmental stress on crops. Biochar is often applied with nutrient addition, impacting mycorrhizal communities. To understand how mycorrhizas explore soils containing biochar, we buried packets of non-activated biochar in root exclusion mesh bags in contrasting agricultural soils. In this greenhouse experiment, with quinoa (Chenopodium quinoa) as the host plant, we tested impacts of mineral nutrient (as manure and fertilizer) and biochar addition on mycorrhizal colonization of biochar. Paraglomus appeared to dominate the biochar packets, and the community of AMF found in the biochar was a subset (12 of 18) of the virtual taxa detected in soil communities. We saw differences in AMF community composition between soils with different edaphic properties, and while nutrient addition shifted those communities, the shifts were inconsistent between soil types and did not significantly influence the observation that Paraglomus appeared to selectively colonize biochar. This observation may reflect differences in AMF traits, with Paraglomus previously identified only in soils (not in roots) pointing to predominately soil exploratory traits. Conversely, the absence of some AMF from the biochar implies either a reduced tendency to explore soils or an ability to avoid recalcitrant nutrient sources. Our results point to a selective colonization of biochar in agricultural soils.

Bacterial-fungal interactions and response to heavy metal contamination of soil in agricultural areas.

Long-term heavy metal contamination of soil affects the structure and function of microbial communities. The aim of our study was to investigate the effect of soil heavy metal contamination on microorganisms and the impact of different heavy metal pollution levels on the microbial interactions. We collected soil samples and determined soil properties. Microbial diversity was analyzed in two groups of samples using high-throughput sequencing technology. Additionally, we constructed microbial networks to analyze microbial interactions. The pollution load index (PLI) < 1 indicates that the area is not polluted. 1 < PLI < 2 represents moderate pollution. PLI was 1.05 and 0.14 for the heavy metal contaminated area and the uncontaminated area, respectively. Cd, Hg, Pb, Zn, and Cu were identified as the major contaminants in the contaminated area, with the contamination factors were 30.35, 11.26, 5.46, 5.19, and 2.46, respectively. The diversities and compositions of the bacterial community varied significantly between the two groups. Compared to the uncontaminated area, the co-occurrence network between bacterial and fungal species in the contaminated area was more complex. The keystone taxa of the co-occurrence network in the contaminated area were more than those in the uncontaminated area and were completely different from it. Heavy metal concentrations played a crucial role in shaping the difference in microbial community compositions. Microorganisms adapt to long-term and moderate levels of heavy metal contamination through enhanced interactions. Bacteria resistant to heavy metal concentrations may play an important role in soils contaminated with moderate levels of heavy metals over long periods of time.

Multi-method approach identifies a South African estuary as an important elasmobranch habitat and potential nursery ground

Elasmobranchs play important ecological roles but are highly threatened. Understanding their habitat use and abundance is crucial for the management and conservation of these species and their habitats. While some species are known to use estuaries as vital habitats (e.g. feeding or nursery grounds), this remains an understudied area. A multi-method approach was used to survey the Keurbooms Estuary on the south coast of South Africa, over two years, to quantify the diversity, relative abundance and habitat use of elasmobranchs in this system. The survey methods were baited remote underwater video (BRUV), boat-based visual sightings, and unmanned aerial video (UAV). Opportunistic sightings were also collected. Six elasmobranch species were observed, with significant differences in community composition between the methods. Whereas effort was skewed towards BRUV surveys, the boat and UAV surveys recorded more elasmobranchs more frequently, and opportunistic sightings recorded the highest diversity. The common eagle ray Myliobatis aquila was the most abundant elasmobranch species and the only one recorded year-round; most individuals (93%) were juveniles, suggesting the Keurbooms Estuary may be a nursery area for this Critically Endangered species. The duckbill ray Aetomylaeus bovinus and common smoothhound shark Mustelus mustelus were observed during summer, the latter forming large aggregations. Another three ray species were recorded rarely. This study highlights the benefit of using a multi-method survey approach for shallow ecosystems and reveals the Keurbooms Estuary as an important habitat for elasmobranchs.

Bacterial Community Structure of Typical Lake Sediments in Yinchuan City and Its Response to Heavy Metals

Lake wetlands are extremely important and special ecosystems, which are important for regional water resource storage, environmental protection, and biodiversity maintenance. Sediment bacteria are an important component of lake ecosystems and are a major driver of biogeochemical cycling in lakes. In order to investigate the community structure of bacteria in typical lake sediments in Yinchuan City and their influencing factors, three typical lakes in Yinchuan City (Yuehai Lake, Mingcui Lake, and Xiniu Lake) were selected for the study and surface sediments were collected in January, April, July, and October 2021. The composition of the sediment bacterial community was examined using 16S rDNA high-throughput sequencing technology, and the response relationships between them and heavy metals were explored. The results showed that the ecological hazard coefficient for heavy metals in the sediments of three typical lakes in Yinchuan City was far less than 40, and the ecological hazard index was far less than 150, all of which indicated a minor ecological hazard. There were no significant differences in bacterial community diversity among the three lakes, but there were significant variations in diversity among the lakes in different seasons and significant differences in community composition. The dominant phyla (top three in terms of relative abundance) in Yuehai Lake, Mingcui Lake, and Xiniu Lake were Proteobacteria, Bacteroidetes, and Chloroflexi. The dominant lower orders were Gammaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria. The main divergent species that occurred at the phylum level in typical lakes in Yinchuan were Proteobacteria, Bacteroidetes, Euryarchaeota, Firmicutes, Actinobacteria, and Acidobacteria. The sediment bacterial community structure of Yuehai Lake was significantly correlated with Cu, Fe, Mn, Zn, As, and Pb; the sediment bacterial community structure of Lake Mingcui was significantly correlated with Fe, Pb, and Cr; and the sediment bacterial community structure of Xiniu Lake was not significantly correlated with heavy metals. The types and contents of sediment heavy metals had a significant effect on the bacterial community structure of sediments in Yinchuan Yuehai Lake and Mingcui Lake and were important environmental factors that caused changes in the bacterial community structure of lake sediments.

Sterile sentinels and MinION sequencing capture active soil microbial communities that differentiate crop rotations

BackgroundSoil microbial communities are difficult to measure and critical to soil processes. The bulk soil microbiome is highly diverse and spatially heterogeneous, which can make it difficult to detect and monitor the responses of microbial communities to differences or changes in management, such as different crop rotations in agricultural research. Sampling a subset of actively growing microbes should promote monitoring how soil microbial communities respond to management by reducing the variation contributed by high microbial spatial and temporal heterogeneity and less active microbes. We tested an in-growth bag method using sterilized soil in root-excluding mesh, “sterile sentinels,” for the capacity to differentiate between crop rotations. We assessed the utility of different incubation times and compared colonized sentinels to concurrently sampled bulk soils for the statistical power to differentiate microbial community composition in low and high diversity crop rotations. We paired this method with Oxford Nanopore MinION sequencing to assess sterile sentinels as a standardized, fast turn-around monitoring method.ResultsCompared to bulk soil, sentinels provided greater statistical power to distinguish between crop rotations for bacterial communities and equivalent power for fungal communities. The incubation time did not affect the statistical power to detect treatment differences in community composition, although longer incubation time increased total biomass. Bulk and sentinel soil samples contained shared and unique microbial taxa that were differentially abundant between crop rotations.ConclusionsOverall, compared to bulk soils, the sentinels captured taxa with copiotrophic or ruderal traits, and plant-associated taxa. The sentinels show promise as a sensitive, scalable method to monitor soil microbial communities and provide information complementary to traditional soil sampling.