Shifts In Community Structure Research Articles

A Unique 100 Meter Underwater Survey Method Documents Changes in Abundance, Richness, and Community Structure of Hawaiʹi Reef Fishes

Hawai′i coral reefs are essential ecosystems providing resources in the form of food and recreation as well as stabilizing nearshore biodiversity. The Seattle Aquarium has exhibited Hawai′i reef fishes and corals since the mid-1980s to educate guests about these critical ecosystems. In 2009, and in collaboration with Hawai′i’s Division of Aquatic Resources (DAR) and Washington State University, the aquarium expanded its conservation work in Hawai′i through annual surveying of eight reefs along the west coast of Hawai′i via SCUBA-based diver operated video (DOV). Five of the sites are in areas partially closed to most fishing while three sites are in areas partially open to most fishing. 100-meter DOV surveys took place a meter above a horizontal or vertical reef, and survey locations were marked with GPS and fixed underwater markings to enable annual surveys to occur in the same locations. Counts of fish species were subsequently made from the archived video. Over the 11 year dataset we documented increased total abundance at all sites and periods of increasing and decreasing species richness. Multivariate analyses comparing fish community structure before (2009-2012) and after an anomalous warm-water event (2013-2019) documented a persistent shift in community structure. This coincides with a documented marine heat wave in Hawai′i and associated coral bleaching events between 2013-2016. These results suggest that our long-term monitoring program captured a phase shift in community structure associated with changing environmental conditions. These persistent shifts may thus indicate hysteresis at relatively short temporal scales, and ongoing monitoring is required to observe whether the systems shift back to the pre-2013 community structure. As coral reef ecosystems face a multitude of stressors from warming waters to marine pollution, long-term monitoring programs are essential to illuminate trends that may inform conservation and management strategies to preserve these imperiled ecosystems.

Biochar induces mineralization of soil recalcitrant components by activation of biochar responsive bacteria groups

Amendment of soil with biochar induces a shift in microbial community structure and promotes faster mineralization of soil organic carbon (SOC), thus offsetting C sequestration effects. Whether biochar induces losses of labile or persistent SOC pools remains largely unknown, and the responsible decomposers await identification. Towards addressing these ends, a C3 soil was amended with Biochar500 or Biochar600 (pyrolyzed at 500 °C and 600 °C, respectively) produced from a C4-maize feedstock and incubated for 28 days. Combination of stable isotope 13C techniques, high-throughput sequencing and Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) allowed changes in soil chemodiversity and biodiversity, as well as their interactive effects on biochar induced SOC mineralization to be elucidated. Results indicated that: i) biochar addition shifted the bacterial community towards dominance of Gemmatimonadetes, Bacteroidia, Alphaproteobacteria and Gammaproteobacteria classes, and coincidence with recalcitrant C components and neutral pH soil; ii) the persistent DOM components (such as condensed aromatics and tannin) were depleted in biochar amended soils, while labile DOM components (such as unsaturated hydrocarbons, lipids, carbohydrates and proteins/amino sugar) were relatively enriched, and; iii) Biochar600 promoted additional soil derived CO2 carbon loss over 28 days (93 mg C kg−1 soil). Collectively, these results suggested that the majority of soil derived CO2 efflux in biochar amended soils originated from recalcitrant components that were mineralized by the persistent organic matter decomposers. This research highlights the significance of biochar responsive taxa in changes of DOM chemodiversity and potential loss of SOC via mineralization.

PLFA Profiling of Coal Mine Spoil: An Integrated Approach for the Assessment of Ecological Restoration

Coal mine overburden spoil created aftermath of mining activities represents disequilibrated geomorphic system. The pedodiversity including its link with biodiversity and landscape ecology describe the spatial diversity has emerged as functional determinants of ecosystem processes. Being the driving force mediating soil processes, ecosystem restoration through mine spoil genesis is monitored based on the shift in microbial community structure in different age series coal mine spoil. Phospholipid fatty acid analysis is culture-independent approach, which provides a set of molecular markers to determine microbial community composition and discriminate microbial communities of different origin. PLFAs are synthesized during microbial growth, rapidly degraded following cell death and reliably reflect living microbial communities. Relative distribution of 51 PLFAs revealed significant variation in microbial community structure across the sites with Shannon diversity index varies from 1.5265 (OB0) to 2.0139 (OB15) and Pielous evenness index from 0.4110 (OB0) to 0.5260 (OB15). Fungal to bacterial ratio exhibited an increasing trend from OB0 (0.055) to OB15 (0.348) over time, which revealed the sign of mine spoil genesis. The principal component analysis and redundancy analysis discriminate different age series coal mine spoil into independent clusters, which evaluated the broad scale patterns of microbial community structure influencing the pace and progress of mine spoil genesis.

Watershed-scale liming reveals the short- and long-term effects of pH on the forest soil microbiome and carbon cycling.

Soil microbial community composition routinely correlates with pH, reflecting both direct pH effects on microbial physiology and long-term biogeochemical feedbacks. We used two watershed-scale liming experiments to identify short- (2 years) and long-term (25 years) changes in the structure and function of bacterial and fungal communities in organic horizons (Oe and Oa ) of acid forest soils. Liming increased soil pH, extractable calcium, and soil carbon stocks, reduced biomass-specific respiration, and caused major changes in the soil microbiome in the short and long term. More taxa responded to liming in the short term (70%) than in the long term (30%), with most showing consistent directional responses at both sites. The ratio of change in relative abundance between limed and reference sites was twofold higher at the long than the short-term site, indicating that the effects of liming grew over time. Liming impacts were most pronounced in fungi, as steep declines of dominant ectomycorrhizal fungi (Cenococcum and Russula) occurred at both sites. Liming favoured neutrophilic bacteria over acidophilic populations according to estimated environmental pH optima. Collectively, these results demonstrate that a liming-induced change of one pH unit has an immediate and persistent effect on the structure and function of microbial communities in acid forest soils. The corresponding suppression of respiration indicates that anthropogenic alterations of soil pH, as driven by acid deposition or liming, can affect forest floor C stocks due to pH-driven shifts in community structure.

A New Ocean State After Nuclear War

AbstractNuclear war would produce dire global consequences for humans and our environment. We simulated climate impacts of US‐Russia and India‐Pakistan nuclear wars in an Earth System Model, here, we report on the ocean impacts. Like volcanic eruptions and large forest fires, firestorms from nuclear war would transport light‐blocking aerosols to the stratosphere, resulting in global cooling. The ocean responds over two timescales: a rapid cooling event and a long recovery, indicating a hysteresis response of the ocean to global cooling. Surface cooling drives sea ice expansion, enhanced meridional overturning, and intensified ocean vertical mixing that is expanded, deeper, and longer lasting. Phytoplankton production and community structure are highly modified by perturbations to light, temperature, and nutrients, resulting in initial decimation of production, especially at high latitudes. A new physical and biogeochemical ocean state results, characterized by shallower pycnoclines, thermoclines, and nutriclines, ventilated deep water masses, and thicker Arctic sea ice. Persistent changes in nutrient limitation drive a shift in phytoplankton community structure, resulting in increased diatom populations, which in turn increase iron scavenging and iron limitation, especially at high latitudes. In the largest US‐Russia scenario (150 Tg), ocean recovery is likely on the order of decades at the surface and hundreds of years at depth, while changes to Arctic sea‐ice will likely last thousands of years, effectively a “Nuclear Little Ice Age.” Marine ecosystems would be highly disrupted by both the initial perturbation and in the new ocean state, resulting in long‐term, global impacts to ecosystem services such as fisheries.

Precipitation variations, rather than N deposition, determine plant ecophysiological traits in a desert steppe in Northern China

Understanding how plant ecophysiological traits of coexisting species within a community respond to environmental changes could help to predict the shift in plant community structure and function, but it remains limited in the scenarios of co-occurring precipitation variations and N deposition. A two-year field experiment was conducted to explore the effects of large precipitation changes (reduced and increased precipitation amount by 25% and 50% relative to ambient control) and high N deposition (10 g N m−2 yr−1) on a series of leaf ecophysiological traits of three dominant species (Stipa tianschanica, a C3 grass; Cleistogenes squarrosa, a C4 grass; and Artemisia capillaris, a C3 forb) in a desert steppe in Northern China. Increasing precipitation significantly linearly promoted the leaf light-saturated photosynthesis rate (Asat) and N use efficiency of the two C3 species, irrespective of N addition. The rises in Asat of both C3 species were mainly caused by increased soil moisture, which strongly induced increases in leaf stomatal conductance (gs) and declines in quantum yield of photosystem II (ΦPSII). However, the Asat of the two C3 species was weakly correlated with their specific leaf area and leaf N concentration, whereas the Asat of the C4 grass was negatively related to its leaf N. Moreover, the Asat, height, and aboveground biomass of the forbs were much more water-sensitive than those of both grass species, with a consequence of the most dominant species turning from grass to forbs as precipitation increased. Our findings highlight that water limitation, rather than N deficit, is the largest factor controlling plant growth in drylands, and plant species-specific ecophysiological responses to precipitation fluctuations will cause a substantial shift in the production and composition of plant community.

Metabarcoding of organic tea (Camellia sinensis L.) chronosequence plots elucidates soil acidification-induced shifts in microbial community structure and putative function

Tea (Camellia sinensis L.) agroecosystem soil acidification (TASA) is occurring at epidemic rates relative to other crops, however TASA remains poorly defined in its pathogenesis and effects on soil microbiota. The present study examined bulk soil physicochemical and bacterial 16S rDNA sequence data to elucidate TASA-associated changes through 10 tea agroecosystem sites, including an organic-certified tea field chronosequence of 3-year- (Young), 8-year- (Middle), and 13-year-old (Old) plots. Soil pH declined linearly with age through chronosequence plots. Hierarchical clustering based on community β-diversity revealed a tipping point in community composition as soil acidified below pH 4.5, which had occurred between Middle and Old plots. Tipping point-associated changes in predicted community functionality included a precipitous decline in nitrogenase-encoding communities and concurrent proliferations of Al-detoxifiers, anti-oxidative specialists, and pathogen virulence factor-encoding communities. PERMANOVA modeling revealed that Streptomyces was the genus with population abundance corresponding most significantly with whole microbiome composition at both OTU- (r2 = 0.460, p < 0.001) and genus-levels (r2 = 0.512, p < 0.001), despite ranking 74th in total abundance among 186 core genera, providing computationally-modeled evidence of a keystone role of Streptomyces under tea agroecosystem conditions. Correlations of soil pH with Rhizobiales (r = 0.713, p < 0.001), Acidibacter (r = −0.717, p < 0.001), and predicted β-glucosidase-encoding communities (r = −0.622, p < 0.001) across all samples indicated potential utility as community-level TASA biomarkers. Moreover, two phylogenetically diverse OTU co-abundance modules also corresponded (p < 0.01) with soil pH across all samples, suggesting that TASA-induced shifts were interfaced by networks of diverse and interactive taxa, or keystone guilds. Presently, organic management per se was unable to retain soil pH within the optimal range for tea plant cultivation (pH 4.5–5.5), therefore additional considerations not currently encompassed by organic management guidelines, such as lower tea planting density, may be necessary to avoid the detrimental effects of soil acidification described above. Moreover, future studies may seek to further elucidate the keystone functions of Streptomyces spp. under tea agroecosystem conditions.

Spread ofBambusa bambos(L.) Voss influences litter‐dwelling arthropod communities in native forests: a case study from Sri Lanka

Both native and non-native bamboo populations can expand their distributions in a rather irregular manner, inflicting changes in native vegetation with potential consequences for litter-dwelling arthropod communities. To our knowledge, no studies have been undertaken to explore the impacts of bamboo spread on litter-dwelling arthropods. This study examined the impacts of Bambusa bambos, a spreading native bamboo species, on abundance and order richness of litter-dwelling arthropods in tropical moist evergreen forests. Bamboo-rich and non-bamboo forests were compared in three study sites at Moragahakanda in the Central Province of Sri Lanka. Arthropods were sampled from leaf litter and individuals were categorised into their respective orders. Arthropod abundance and order richness were higher in bamboo-rich forests than in non-bamboo forests across all sites, indicating more hospitable micro-habitat conditions following bamboo spread. Litter-dwelling arthropods belonging to orders Blattodea, Hymenoptera, Diptera, Lepidoptera and Orthoptera were either more prevalent or more frequently associated with bamboo-rich forests than non-bamboo forests, suggesting a potential shift in community structure. The abundance and order richness of litter-dwelling arthropods in non-bamboo forests was explained by environmental variables, whilst no such associations were observed in bamboo-rich forests. The overall findings indicate that the spread of bamboo may facilitate litter-dwelling arthropods and cause a compositional shift in taxonomic assemblages, perhaps as a result of changes in the micro-habitat conditions on the forest floor.

Effects of alder- and salmon-derived nutrients on aquatic bacterial community structure and microbial community metabolism in subarctic lakes.

Alder (Alnus spp.) and Pacific salmon (Oncorhynchus spp.) provide key nutrient subsidies to freshwater systems. In southwestern Alaska, alder-derived nutrients (ADNs) are increasing as alder cover expands in response to climate warming, while climate change and habitat degradation are reducing marine-derived nutrients (MDNs) in salmon-spawning habitats. To assess the relative influences of ADN and MDN on aquatic microbial community structure and function, we analyzed lake chemistry, bacterial community structure, and microbial metabolism in 13 lakes with varying alder cover and salmon abundance in southwestern Alaska. We conducted bioassays to determine microbial nutrient limitation and physical factors modulating microbial response to nutrient inputs (+N, +P and +NP treatments). Seasonal shifts in bacterial community structure (F = 7.47, P < 0.01) coincided with changes in lake nitrogen (N) and phosphorus (P) concentrations (r2 = 0.19 and 0.16, both P < 0.05), and putrescine degradation (r2 = 0.13, P = 0.06), suggesting the influx and microbial use of MDN. Higher microbial metabolism occurred in summer than spring, coinciding with salmon runs. Increased microbial metabolism occurred in lakes where more salmon spawned. Microbial metabolic activity was unrelated to alder cover, likely because ADN provides less resource diversity than MDN. When nutrients were added to spring samples, there was greater substrate use by microbial communities from lakes with elevated Chl a concentrations and large relative catchment areas (β estimates for all treatments > 0.56, all P < 0.07). Thus, physical watershed and lake features mediate the effects of nutrient subsidies on aquatic microbial metabolic activity.

Shifts of microbial community structure along substrate concentration gradients in immobilized biomass for nitrogen removal

Immobilized biomass technology has been regarded as an effective strategy to enhance simultaneous nitrification and denitrification (SND) in existing aerobic biological wastewater treatment processes. Nevertheless, the mechanisms of SND in an aerobic immobilized biomass need to be proven. In this study, waste sludge from municipal wastewater treatment plants was immobilized by cellulose triacetate as bioplates, and an immobilized bioplate reactor (IBPR) was successfully established for nitrogen removal tests. The SND efficiency of the IBPR was increased 18% under the intermittent aeration (IA) mode compared with that under the continuous aeration (CA) mode. During IA operation, the IBPR achieved 96% COD removal and 76% NH4+-N removal, with 71% SND. The results of microbial community analysis by high-throughput sequencing showed that nitrogen-related functional bacteria were more abundant in the bioplates than in the attached biofilms. The colocalization of nitrifiers and denitrifiers in the bioplates was observed, and the microbial community of nitrogen-related functional bacteria clearly shifted with the substrate concentration gradients.

Influence of bottom seawater oxygen on archaeal tetraether lipids in sediments: Implications for archaeal lipid-based proxies

Glycerol dibiphytanyl glycerol tetraethers (GDGTs) are important archaeal membrane lipids that widely occur in marine water columns and sediments. Based on its sensitivity to temperature, the paleotemperature index TEX86 was developed and extensively studied. However, GDGTs in sediments are not only affected by their external sources, but also by internal biochemical processes. The effect of bottom water redox conditions on GDGT composition and TEX86 in the surface sediments remains unclear. In this study, field investigations in the eastern China marginal seas were conducted to trace the responses of sedimentary GDGTs to bottom dissolved oxygen (DO). Our results showed that the TEX86 was independent of the DO level. However, the decrease in DO was accompanied by an increase in GDGT Ring Index (RI) and relative abundance of crenarchaeol (Cren) in contrast to the decrease pattern for GDGT-0, suggesting that DO has important effects on the composition of GDGTs but shows limited impact on TEX86 in the study area. These changes were probably driven by archaeal adaptation, shift of community structure and degradation of GDGTs. In addition, strong relationships between DO and RI and between DO and GDGT abundances (i.e., %GDGT-0, GDGT-0/Cren) indicate that these parameters can be used as potential redox proxies for bottom water, especially in relatively stable stratified waters. Further studies coupled with archaeal community are needed to cover more areas to constrain their applicability and driving mechanisms.

Combined read- and assembly-based metagenomics to reconstruct a Dehalococcoides mccartyi genome from PCB-contaminated sediments and evaluate functional differences among organohalide-respiring consortia in the presence of different halogenated contaminants.

Microbial communities that support respiration of halogenated organic contaminants by Dehalococcoides sp. facilitate full-scale bioremediation of chlorinated ethenes and demonstrate the potential to aid in bioremediation of halogenated aromatics like polychlorinated biphenyls (PCBs). However, it remains unclear if Dehalococcoides-containing microbial community dynamics observed in sediment-free systems quantitatively resemble that of sediment environments. To evaluate that possibility we assembled, annotated, and analyzed a Dehalococcoides sp. metagenome-assembled genome (MAG) from PCB-contaminated sediments. Phylogenetic analysis of reductive dehalogenase gene (rdhA) sequences within the MAG revealed that pcbA1 and pcbA4/5-like rdhA were absent, while several candidate PCB dehalogenase genes and potentially novel rdhA sequences were identified. Using a compositional comparative metagenomics approach, we quantified Dehalococcoides-containing microbial community structure shifts in response to halogenated organics and the presence of sediments. Functional level analysis revealed significantly greater abundances of genes associated with cobamide remodeling and horizontal gene transfer in tetrachloroethene-fed cultures as compared to halogenated aromatic-exposed consortia with or without sediments, despite little evidence of statistically significant differences in microbial community taxonomic structure. Our findings support the use of a generalizable comparative metagenomics workflow to evaluate Dehalococcoides-containing consortia in sediments and sediment-free environments to eludicate functions and microbial interactions that facilitate bioremediation of halogenated organic contaminants.

Southern Ocean Phytoplankton Stimulated by Wildfire Emissions and Sustained by Iron Recycling

AbstractLarge ash plumes emitted by the 2019–2020 Australian wildfires were associated with a widespread phytoplankton bloom in the iron‐limited Pacific sector of the Southern Ocean. In this study, we used satellite observations and aerosol reanalysis products to study the regional phytoplankton community response to wildfire emissions. The bloom was stimulated by pyrogenic iron fertilization and coincided with elevated cellular pigment concentrations, increased photochemical efficiency, and apparent community structural shifts. Physiological anomalies were consistent with previously observed phytoplankton responses to iron stress relief and persisted for up to 9 months. Supported by a regional iron budget, we conclude that the bloom was sustained by iron recycling and episodic inputs of pyrogenic and dust‐borne mineral iron. The continuous regeneration of iron was likely facilitated by the bloom's large size, mitigating edge dilution effects, as well as enhanced bioavailability of pyrogenic and mineral iron due to atmospheric and chemical processing during long‐range transport.

Changes to the structure and function of microbial communities in Spartina alterniflora and Kandelia obovata sediments as a factor of stand age

The effects of Kandelia obovata introduction and Spartina alterniflora invasion on the microorganisms are very important for coastal ecology and restoration. MiSeq sequencing of the 16S rRNA gene and Tax4Fun predictive functional profiles were used to investigate the diversity estimators, community structures and potential metabolic functions of benthic bacteria in surface sediments of coastal wetlands invaded by S. alterniflora and artificially planted with K. obovata at stand ages of 2-, 8-, 11-, 16- and 60-years on Ximen Island, Yueqing Bay, China. The results showed that the sediment bacterial richness was significantly decreased in 60-year K. obovata stands compared with younger K. obovata stands and S. alterniflora stands. The age of K. obovata and specie of exotic plants formed distinct bacterial communities and functional structures in sediments, respectively. With increasing plantation of K. obovata, the bacterial communities shifted from the class Anaerolineae, the genus Sulfurovum, and bacteria involved in sulfate reduction as abundant taxa to higher proportions of bacteria involved in degradation of plant polysaccharide and nitrate reduction. The shift in bacterial community structures was mainly driven by changes in sediment total organic matter, total nitrogen, total phosphorus, ammonium concentrations, pH and temperature. The community functions also changed from nitrogen fixation to more nitrate reduction and denitrification processes. Compared with 60-year K. obovata, S. alterniflora was occupied by higher proportions of the phylum Bacteroidetes, the orders Rhodobacterales, Flavobacteriales and Desulfuromonadales, and total nitrogen, total phosphorus concentrations and sediment temperature were major environmental factors affecting the variation. Among the major sulfur cycling processes examined, higher potential of dissimilatory sulfate reduction was observed in S. alterniflora. Our results indicated that K. obovata introduction has a greater effect on the bacterial community diversity and structure than S. alterniflora invasion. This study could improve the understanding of microbial processes and potential functions of K. obovata introduction and S. alterniflora invasion and provide reference in the restoration and management of the coastal wetlands.

Nano-hydroxyapatite increased soil quality and boosted beneficial soil microbes

Nano-hydroxyapatite (nano-HA) is a promising phosphorus nanofertilizer to be applied in agriculture. Understanding their environmental implications is important for their safe and sustainable use. In this study, maize plants were cultivated in soil amended with nano-HA at 150 mg P per kg soil for 4 weeks. The impacts of nano-HA on plant growth, soil quality, and soil microbial communities were investigated. Nano-HA significantly increased fresh biomass, the content of bioavailable phosphorus, and chlorophyll content of maize plants, indicating the positive effects of nano-HA on plant growth. In addition, nano-HA increased soil quality by increasing soil bioavailable P (12.7-fold), electrical conductivity (EC) (28.7%) and soil organic matter (SOM) (15.6%). Gas chromatography–mass spectrometry (GC–MS) based soil metabolomics revealed that nano-HA increased the content of many low molecular weight metabolites in soil, e.g., sugar and sugar alcohols ( D -arabinose, L -arabitol, palatinitol, and sorbitol), amino acids ( L -tyrosine), and phenolic acids (catechin and scopoletin). The sequencing of 16S rRNA reveals that nano-HA exposure didn’t alter the richness of soil microbial communities. However, nano-HA induced a shift in soil bacterial community structure; groups related to plant growth-promoting rhizobacteria (PGPR), especially P solubilizing bacteria (PSB), e.g., Burkholderiaceae , Massilia , Sinomonas , and Streptomyces have been increased . The results of this study provide a holistic evaluation of the effects of nano-HA on plant growth and soil health.

Microbial communities along the soil-root continuum are determined by root anatomical boundaries, soil properties, and root exudation

The microbiome in plant-soil systems has a significant influence in promoting plant growth. Despite this, the extent of selectivity that the plant exerts on the microbiome in the continuum between the soil and internal plant tissues is not well understood. This study analysed the root microbiome of a legume, Melilotus officinalis (L.) Pall., sweet clover, and focused on dynamic shifts in the microbial community structure through the niches of bulk soil, rhizosphere, periderm, phloem and xylem, and further examined the effects of soil factors, root exudate metabolism, and root cell wall development on microbiome assemblages in different root compartments. Young and mature plants were sampled at 24 field sites and the microbial communities in different niches from bulk soil and rhizosphere through to root compartments were analysed by 16S rRNA gene sequencing. The microbiome composition changed from periderm to phloem to a greater extent than across other boundaries. Variation in microbiome composition was associated with geographic distance and soil properties for the bulk soil, rhizosphere and periderm niches. Root exudation influenced the rhizosphere microbiome assemblages in young and mature plants. The endophyte communities that occupied the phloem and xylem were most conserved and were independent of growing environments and root exudation. Symbiotic rhizobia able to nodulate M. officinalis were prominent colonisers of the periderm (∼15%) and xylem (∼6.2%), but were only a minor component in other soil-related niches (0.1%–2.5%). In xylem tissues, endophyte diversity was correlated with the total cell wall and lignin content across the sampled sites (r = 0.29–0.62). Our results demonstrate that selection of microbiome constituents occurs at different boundaries through bulk soil, rhizosphere, periderm, phloem and xylem, and is especially strong across the periderm boundary. The conserved endophyte community in the innermost tissues (phloem and xylem) was identified, and will be potentially advantageous to the development of specific beneficial microbial inoculants.

The impact of different voltage application modes on biodegradation of chloramphenicol and shift of microbial community structure

The impact of different voltage application modes on biodegradation of chloramphenicol and shift of microbial community structure

Salinity affects microbial composition and function in artificially induced biocrusts: Implications for cyanobacterial inoculation in saline soils

Cyanobacterial inoculation is a promising technology that can induce biocrust development, for stabilizing degraded soils in dryland environments. However, it is challenging to grow cyanobacteria in dry, saline soils, which limits the application of this technology. In this study, NaCl was added into field-collected induced biocrusts to investigate how salt affects the biocrust community. This fundamental knowledge improves our assessment of microbial salinity preference and adaptation, and can guide researchers to select the appropriate cyanobacterial inoculants for saline soil restoration. The results showed that the biocrusts induced by inoculating Microcoleus vaginatus and Scytonema javanicum could survive 1.0% salinity, although both salt and drought stresses significantly inhibited microbial biomass and metabolism (P < 0.05), and salinity led to an obvious shift in microbial community structure. Compared to salt stress, drought seems to provide a vital ecological protection for the biocrusts, allowing them to be active only under relative low salinity after hydration. In the induced biocrusts, cyanobacteria were always the dominant organisms (even 18 years since inoculation), whereas under elevated salinity, cyanobacterial communities with lower relative abundance had a higher survival percentage of M. steenstrupii and Phormidium sp. Altogether, our results showed that both prokaryotic and eukaryotic communities have obvious salinity preference in the cyanobacteria-induced biocrusts. These results suggest that cyanobacterial inoculation strategies can be adapted in response to the soil salinity conditions. Furthermore, a combined inoculation of M. steenstrupii and Phormidium sp. appears to be favorable approach that is expected to improve cyanobacterial inoculation technology in saline soils.

Forage fish as a predator: summer and autumn diet of Atlantic herring in Trinity Bay, Newfoundland

Atlantic herring (Clupea harengus; hereafter herring) is a forage fish that transfers energy from lower to higher trophic levels and sustains high-volume fisheries in the North Atlantic. This study aims to improve our understanding of the ecology of Newfoundland herring and its vulnerability to climate change by identifying key prey items and describing adult herring feeding strategies. We compared plankton assemblages to stomach content and stable isotope analyses from herring collected in Trinity Bay, Newfoundland, in late summer and autumn 2017–2019. Six distinct zooplankton communities were identified across all years, with a shift in community structure in September 2018. This shift coincided with a change from fresher, warmer waters (12–17 °C) to more saline, cooler waters (10.5 °C). The most frequently consumed prey items were amphipods (Themisto spp.) and calanoid copepods (primarily Calanus and Temora spp.). Fish eggs, larvae, and juveniles, primarily identified as capelin, were observed in stomach contents in all years. Fish contributed most to diets in 2017, which corresponded with the peak year for larval densities in Trinity Bay, suggesting that piscivory may increase at higher larval densities. Herring were opportunistic feeders, although some individuals exhibited selective feeding on copepods, amphipods, euphausiids, and the early life stages of fishes. Stable isotope analyses supported the finding that herring piscivory is prevalent in eastern Newfoundland. Given its adaptive feeding strategy and wide range of consumed prey, we conclude that adult Newfoundland herring is resilient to bottom-up changes observed in the environment.

Best practices in metabarcoding of fungi: From experimental design to results.

The development of high-throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems. Here we provide an overview of current best practices in metabarcoding analysis of fungal communities, from experimental design through molecular and computational analyses. By reanalysing published data sets, we demonstrate that operational taxonomic units (OTUs) outperform amplified sequence variants (ASVs) in recovering fungal diversity, a finding that is particularly evident for long markers. Additionally, analysis of the full-length ITS region allows more accurate taxonomic placement of fungi and other eukaryotes compared to the ITS2subregion. Finally, we show that specific methods for compositional data analyses provide more reliable estimates of shifts in community structure. We conclude that metabarcoding analyses of fungi are especially promising for integrating fungi into the full microbiome and broader ecosystem functioning context, recovery of novel fungal lineages and ancient organisms as well as barcoding of old specimens including type material.