High Microbial Abundance Research Articles

Holo-Transcriptome Sequences From the Tropical Marine Sponge Cinachyrella alloclada.

Marine sponge transcriptomes are underrepresented in current databases. Furthermore, only 2 sponge genomes are available for comparative studies. Here we present the assembled and annotated holo-transcriptome of the common Florida reef sponge from the species Cinachyrella alloclada. After Illumina high-throughput sequencing, the data assembled using Trinity v2.5 confirmed a highly symbiotic organism, with the complexity of high microbial abundance sponges. This dataset is enriched in poly-A selected eukaryotic, rather than microbial transcripts. Overall, 39 813 transcripts with verified sponge sequence homology coded for 8496 unique proteins. The average sequence length was found to be 946 bp with an N50 sequence length of 1290 bp. Overall, the sponge assembly resulted in a GC content of 51.04%, which is within the range of GC bases in a eukaryotic transcriptome. BUSCO scored completeness analysis revealed a completeness of 60.3% and 60.1% based on the Eukaryota and Metazoa databases, respectively. Overall, this study points to an overarching goal of developing the C. alloclada sponge as a useful new experimental model organism.

Manufacturing triple-isotopically labeled microbial necromass to track C, N and P cycles in terrestrial ecosystems

The functional relevance of microbial necromass in terrestrial biogeochemical cycles remains one of the unresolved mysteries of element cycling in ecosystems, especially considering the high microbial abundance and turnover in soil. We therefore established a protocol to manufacture multi-isotope (14C, 15N and 33P) labeled microbial necromass to comprehensively track the turnover of microbial necromass elements within element cycles. This protocol encompasses the i) microbial cultivation of Pseudomonas kilonensis ACN4 (Gram-negative) and Bacillus licheniformis DSM13 (Gram-positive) on labeled minimal medium as well as fungal cultivation of Hypsizygus tessulatus on a complex yeast medium, ii) quantification of radio- (14C, 33P) and stable (15N) isotope incorporation as well their cellular pool partitioning, and iii) determination of element and tracer isotope uptake efficiency. We achieved 1 g of bacterial biomass per liter minimum medium within 24 h and 2.9 g l−1 fungal biomass in complex medium within 18 d. This production rate enabled us to produce more than 100 g of necromass within only one half-life time of 33P, including post-harvest processing. Isotope uptake and incorporation for 33P ranged from 10 to 73%, for 15N from 24 to 52%, and for 14C from 12 to 23%. Each of the cultivated species showed individual patterns of tracer element uptake. The nutritional value of the carbon- (C), nitrogen- (N) and phosphorus- (P) labeled microbial necromass was characterized by a water-based, necromass species-specific partitioning scheme with subsequent elemental analysis of the pools. We separated Gram-negative, Gram-positive and fungi’s cellular pools to characterize element and tracer partitioning among dissolved versus particulate fractions. That is essential because these properties subsequently affect the respective pool's availability for ecosystem nutrition. Our procedure allows a defined production of microorganism-based necromass, enabling versatile use to determine necromass-related nutrient fluxes in terrestrial ecosystem studies.

Enhancement of algae ponds for rural domestic sewage treatment by prolonging daylight using artificial lamps

Algal ponds (APs) are widely used as treatment facilities for domestic sewage in sparsely populated rural areas. However, few AP studies have focused on daylight length to enhance pollutants removal. In this study, four algae ponds were set up, daylight was prolonged by 0, 2, 4, and 6 h with an illuminating intensity of 3000 lx. The highest removal efficiencies of total nitrogen, ammonium, and total phosphorus were 37.36%, 41.20%, and 21.56% due to the highest microbial abundance under optimum conditions (2 h PD), respectively. Excessive PD (4 h and 6 h) could inhibit the removal abilities. PD also increased the maximum relative electron transport rate of algae, leading to an increase in the photosynthetic capacity of APs. Meanwhile, the high microbial abundance indicates that chemoheterotrophic bacteria are the main influencing factor for the removal of nitrogen and phosphorus by the APs. Moreover, the system with PD using artificial lamps was proven to be feasible for engineering applications and potentially utilized in rural domestic wastewater treatment.

Comparative analysis of the serum microbiome of HIV infected individuals

HIV infects the CD4 cells which marks the suppression of our immune system. DNA from serum of healthy, treated and untreated HIV infected individuals was extracted. The DNA was subjected to 16S metagenomic sequencing and analyzed using QIIME2 pipeline. 16S sequencing analysis showed serum microbiome was dominated by Firmicutes, Proteobacteria, Bacteroidota and Actinobacteria. Treated HIV infection showed highest abundance of Firmicutes (66.40%) significantly higher than untreated HIV infection (35.88%) and control (41.89%). Bacilli was most abundant class in treated (63.59%) and second most abundant in untreated (34.53%) while control group showed highest abundance of class Gamma-proteobacteria (45.86%). Untreated HIV infection group showed Enterococcus (10.72%) and Streptococcus (6.599%) as the most abundant species. Untreated HIV infection showed significantly higher (p = 0.0039) species richness than treated and control groups. An altered serum microbiome of treated HIV infection and higher microbial abundance in serum of untreated HIV infection was observed.

Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts.

ABSTRACTThe fossil record indicates that the earliest evidence of extant marine sponges (phylum Porifera) existed during the Cambrian explosion and that their symbiosis with microbes may have begun in their extinct ancestors during the Precambrian period. Many symbionts have adapted to their sponge host, where they perform specific, specialized functions. There are also widely distributed bacterial taxa such as Poribacteria, SAUL, and Tethybacterales that are found in a broad range of invertebrate hosts. Here, we added 11 new genomes to the Tethybacterales order, identified a novel family, and show that functional potential differs between the three Tethybacterales families. We compare the Tethybacterales with the well-characterized Entoporibacteria and show that these symbionts appear to preferentially associate with low-microbial abundance (LMA) and high-microbial abundance (HMA) sponges, respectively. Within these sponges, we show that these symbionts likely perform distinct functions and may have undergone multiple association events, rather than a single association event followed by coevolution.

Mycorrhizal-Assisted Phytoremediation and Intercropping Strategies Improved the Health of Contaminated Soil in a Peri-Urban Area.

Soils of abandoned and vacant lands in the periphery of cities are frequently subjected to illegal dumping and can undergo degradation processes such as depletion of organic matter and nutrients, reduced biodiversity, and the presence of contaminants, which may exert an intense abiotic stress on biological communities. Mycorrhizal-assisted phytoremediation and intercropping strategies are highly suitable options for remediation of these sites. A two-year field experiment was conducted at a peri-urban site contaminated with petroleum hydrocarbons and polychlorinated biphenyls, to assess the effects of plant growth (spontaneous plant species, Medicago sativa, and Populus × canadensis, alone vs. intercropped) and inoculation of a commercial arbuscular mycorrhizal and ectomycorrhizal inoculum. Contaminant degradation, plant performance, and biodiversity, as well as a variety of microbial indicators of soil health (microbial biomass, activity, and diversity parameters) were determined. The rhizosphere bacterial and fungal microbiomes were assessed by measuring the structural diversity and composition via amplicon sequencing. Establishment of spontaneous vegetation led to greater plant and soil microbial diversity. Intercropping enhanced the activity of soil enzymes involved in nutrient cycling. The mycorrhizal treatment was a key contributor to the establishment of intercropping with poplar and alfalfa. Inoculated and poplar-alfalfa intercropped soils had a higher microbial abundance than soils colonized by spontaneous vegetation. Our study provided evidence of the potential of mycorrhizal-assisted phytoremediation and intercropping strategies to improve soil health in degraded peri-urban areas.

Biochemical variability in sponges across the Caribbean basin

AbstractSponges are a diverse phylum of sessile filter‐feeding invertebrates that are abundant on Caribbean reefs and provide essential ecological services, including nutrient cycling, reef stabilization, habitat, and food for a variety of fishes and invertebrates. As prominent members of the benthic community, and thus potential food resources, factors determining the biochemical and energetic content of sponges will affect their trophic contributions to coral reef ecosystems. In order to evaluate the influence of geographic variation on biochemical composition and energetic content in the tissue of sponges, we collected several common and widespread species (Agelas conifera, Agelas tubulata, Amphimedon compressa, Aplysina cauliformis, Niphates amorpha, Niphates erecta, and Xestospongia muta) from multiple shallow reefs in four countries across the Caribbean Basin, including Belize, Curaçao, Grand Cayman, and St. Croix, U.S. Virgin Islands. In addition, we correlated inherent species‐level traits, including the production of antipredator chemical defenses and the relative abundance of microbial symbionts, with biochemical and energetic content. We found that energetic content was higher in sponges with antipredator chemical defenses, and was significantly correlated with the concentration of chemical extracts from these sponges. We also noted that sponges with high microbial abundance contained significantly more soluble protein than sponges with low microbial abundance. Finally, both biochemical and energetic content varied significantly among sponges from different locations; sponges from Grand Cayman had the highest lipid and energetic content, whereas sponges from Belize had the highest carbohydrate content but lowest energetic content. Despite similar environmental conditions at these sites, our results demonstrate that biochemical and energetic content of sponges exhibits geographic variability, with potential implications for the trophic ecology of sponges throughout the Caribbean Basin.

Habitat environmental factors influence intestinal microbial diversity of the short-faced moles (Scaptochirus moschata)

The short-faced moles (Scaptochirus moschata) are unique Chinese mammal that live in burrows for life. They have complex ecological adaptation mechanisms to adapt to perennial underground life. Intestinal microbes play an important role in the ecological adaptation of wild animals. The gut microbiota diversity and its function in short-faced moles’ ecological adaptation is a scientific issue worth exploring. In this study, the Illumina HiSeq sequencing platform was used to sequence the V3-V4 hypervariable regions of the 16S rRNA genes of 22 short-faced moles’ intestinal samples to study the composition and functional structure of their intestinal microbiota. The results showed that in the short-faced moles’ intestine, there are four main phyla, Firmicutes, Proteobacteria, Actinobacteria and Bacteroidete. At the family level, Peptostreptococcaceae and Enterobacteriaceae have the highest abundance. At the genus level, Romboutsia is the genus with the highest microbial abundance. According to the KEGG database, the main functions of short-faced mole gut microbes are metabolism, genetic information processing, environmental information processing, and cellular processes. The function of short-faced mole intestinal microbiota is suitable for its long-term burrowing life. No gender difference is found in the composition and function of the short-faced mole intestinal microbiota. There are significant differences in the composition and functional structure of the short-faced mole gut microbiota between samples collected from different habitats. We conferred that this is related to the different environment factors in which they live, especially to the edaphic factors.

Sponges With Microbial Symbionts Transform Dissolved Organic Matter and Take Up Organohalides

Seawater dissolved organic matter (DOM) is a large reservoir of carbon composed of a complex and poorly characterized mixture of molecules. Sponges have long been known to consume dissolved organic carbon (DOC) from this mixture, but the role of microbial sponge symbionts in this process is complex, and the molecules involved remain largely unknown. In order to better understand how sponge processing changes seawater DOM, we used untargeted metabolomics to characterize DOM in samples of incurrent and excurrent seawater taken from sponges on the fore-reef off Carrie Bow Cay, Belize, over 2 years. We collected samples from three sponge species each with either high or low microbial abundance (HMA, LMA) to explore the relationship between symbiont abundance and DOM alterations. Analyses revealed that sponges took up metabolites and changed the composition of seawater DOM, but only for the three HMA species, and none of the LMA species, implicating microbial symbionts in this uptake. Using a new mass spectra classification tool, we found that putative compositions of features depleted in the excurrent samples of HMA sponges were similar in both years and were dominated by organic acids and derivatives (74%) and organic nitrogen compounds (19%). Interestingly, HMA sponges also took up halogenated compounds (containing chlorine or bromine), providing evidence of a previously unknown mechanism of halide cycling. The metabolites taken up by HMA sponges may be used as a food source or as building blocks of chemical defenses, selective advantages that may have guided the evolution of microbial symbioses in sponges.

Processing of Naturally Sourced Macroalgal- and Coral-Dissolved Organic Matter (DOM) by High and Low Microbial Abundance Encrusting Sponges

Sponges play a key role in (re)cycling of dissolved organic matter (DOM) and inorganic nutrients in coral reef ecosystems. Macroalgae and corals release different quantities of DOM and at different bioavailabilities to sponges and their microbiome. Given the current coral- to algal-dominance shift on coral reefs, we assessed the differential processing of macroalgal- and coral-DOM by three high and three low microbial abundance (HMA and LMA) encrusting sponge species. We followed the assimilation of naturally sourced 13C- and 15N-enriched macroalgal- and coral-DOM into bulk tissue and into host- versus bacteria-specific phospholipid fatty acids (PLFAs). Additionally, we compared sponge-processing of the two natural DOM sources with 13C- and 15N-enriched laboratory-made diatom-DOM. All investigated sponges utilized all DOM sources, with higher assimilation rates in LMA compared to HMA sponges. No difference was found in carbon assimilation of coral- versus macroalgal-DOM into bulk tissue and host- versus bacteria-specific PLFAs, but macroalgal nitrogen was assimilated into bulk tissue up to eight times faster compared to the other sources, indicating its higher bioavailability to the sponges. Additionally, LMA sponges released significantly more inorganic nitrogen after feeding on macroalgal-DOM. Therefore, we hypothesize that, depending on the abundance and composition of the sponge community, sponges could catalyze reef eutrophication through increased turnover of nitrogen under coral-to-algal regime shifts.

Microbial abundance and community in constructed wetlands planted with Phragmites australis and Typha orientalis in winter

In winter, the withering of plants in constructed wetlands (CWs) limits the removal of pollutants by plants. It is prospective to improve performance of CWs through targeted transformation of the microbial abundance and community. This research characterized the purification performance of CWs planted with Phragmites australis (P. australis, PA) and Typha orientalis (T. orientalis, TO) and those in the unplanted constructed wetland (CT, control). PA showed some superiority in the removal rates of COD and NH4 +-N (42.06% ± 4.25% and 70.51% ± 1.46%, respectively). The 16S rRNA gene copy numbers (7.60 ± 0.57 × 104 copies/g) and the ammonia oxygen bacteria (5.30 ± 0.06 × 103 copies/g) were the highest in PA. In microbial structure, compared with TO and CT, in addition to common microorganisms that can remove contaminants, many specific functional genera were detected in PA (Rhodobacter, Catellibacterium, Hydrogenophaga, Geothrix and Aeromonas), which promoted the removal of NH4 +-N and COD. Novelty statement The microbial abundance and communities were characterized in CWs with different plant species during winter. Better removal efficiency with high microbial abundance and diversified microbial community were found in CWs planted with Phragmites australis. This study confirmed that in winter, withered plants in CWs can effectively remove NH4 +-N and COD by affecting microbial abundance and community structure.

Subcellular view of host\u2013microbiome nutrient exchange in sponges: insights into the ecological success of an early metazoan\u2013microbe symbiosis

BackgroundSponges are increasingly recognised as key ecosystem engineers in many aquatic habitats. They play an important role in nutrient cycling due to their unrivalled capacity for processing both dissolved and particulate organic matter (DOM and POM) and the exceptional metabolic repertoire of their diverse and abundant microbial communities. Functional studies determining the role of host and microbiome in organic nutrient uptake and exchange, however, are limited. Therefore, we coupled pulse-chase isotopic tracer techniques with nanoscale secondary ion mass spectrometry (NanoSIMS) to visualise the uptake and translocation of 13C- and 15N-labelled dissolved and particulate organic food at subcellular level in the high microbial abundance sponge Plakortis angulospiculatus and the low microbial abundance sponge Halisarca caerulea.ResultsThe two sponge species showed significant enrichment of DOM- and POM-derived 13C and 15N into their tissue over time. Microbial symbionts were actively involved in the assimilation of DOM, but host filtering cells (choanocytes) appeared to be the primary site of DOM and POM uptake in both sponge species overall, via pinocytosis and phagocytosis, respectively. Translocation of carbon and nitrogen from choanocytes to microbial symbionts occurred over time, irrespective of microbial abundance, reflecting recycling of host waste products by the microbiome.ConclusionsHere, we provide empirical evidence indicating that the prokaryotic communities of a high and a low microbial abundance sponge obtain nutritional benefits from their host-associated lifestyle. The metabolic interaction between the highly efficient filter-feeding host and its microbial symbionts likely provides a competitive advantage to the sponge holobiont in the oligotrophic environments in which they thrive, by retaining and recycling limiting nutrients. Sponges present a unique model to link nutritional symbiotic interactions to holobiont function, and, via cascading effects, ecosystem functioning, in one of the earliest metazoan–microbe symbioses.1KyCQaknthx73_ZUqh3faYVideo abstract

Bacterial precursors and unsaturated long-chain fatty acids are biomarkers of North-Atlantic deep-sea demosponges.

Sponges produce distinct fatty acids (FAs) that (potentially) can be used as chemotaxonomic and ecological biomarkers to study endosymbiont-host interactions and the functional ecology of sponges. Here, we present FA profiles of five common habitat-building deep-sea sponges (class Demospongiae, order Tetractinellida), which are classified as high microbial abundance (HMA) species. Geodia hentscheli, G. parva, G. atlantica, G. barretti, and Stelletta rhaphidiophora were collected from boreal and Arctic sponge grounds in the North-Atlantic Ocean. Bacterial FAs dominated in all five species and particularly isomeric mixtures of mid-chain branched FAs (MBFAs, 8- and 9-Me-C16:0 and 10- and 11-Me-C18:0) were found in high abundance (together ≥ 20% of total FAs) aside more common bacterial markers. In addition, the sponges produced long-chain linear, mid- and a(i)-branched unsaturated FAs (LCFAs) with a chain length of 24‒28 C atoms and had predominantly the typical Δ5,9 unsaturation, although the Δ9,19 and (yet undescribed) Δ11,21 unsaturations were also identified. G. parva and S. rhaphidiophora each produced distinct LCFAs, while G. atlantica, G. barretti, and G. hentscheli produced similar LCFAs, but in different ratios. The different bacterial precursors varied in carbon isotopic composition (δ13C), with MBFAs being more enriched compared to other bacterial (linear and a(i)-branched) FAs. We propose biosynthetic pathways for different LCFAs from their bacterial precursors, that are consistent with small isotopic differences found in LCFAs. Indeed, FA profiles of deep-sea sponges can serve as chemotaxonomic markers and support the concept that sponges acquire building blocks from their endosymbiotic bacteria.

The response of microbial community structure and sediment properties to anthropogenic activities in Caohai wetland sediments

This study aimed to investigate the response of sediment microbial communities (including bacteria and archaeal groups) in Caohai Lake to anthropogenic activities. The sediment samples were collected from the regions with high anthropogenic interference and low anthropogenic interference. Their physicochemical properties and enzyme activities were analyzed, and the bacterial and archaeal communities were investigated using high-throughput sequencing technology. The results showed that the physicochemical characters changed by anthropogenic activities were the important factors that influenced enzyme activities, alpha diversity, key functional taxa, and community structure. And the impact of anthropogenic activities on microbial communities might follow a non-linear pattern. Furthermore, few significant differences of alpha indices between the high and low disturbed areas, but clear differences of microbial community composition analysis and beta-diversity analysis were observed. The hypothesis was proved that the intensity of anthropogenic impacts in Caohai had not reached the potential thresholds. The best distinguish biomarkers between the two areas and the most related key nodes among the network did not always have a high microbial abundance. The anthropogenic activities might influence the microbial community by affecting a small number of the key taxon in the ecological network. These findings provided a valuable understanding of how sediment microorganisms respond to anthropogenic activities in Caohai Lake.

Archaeal communities of low and high microbial abundance sponges inhabiting the remote western Indian Ocean island of Mayotte.

Marine sponges are abundant and ecologically important components of coral reefs and have been shown to harbour exceptionally high microbial densities, which can differ substantially among sponge species. However, this dichotomy between high and low microbial abundance (HMA, LMA) sponges is still not fully understood, particularly as concerns the archaeal community. This study aims to fill this gap by analysing (using 454-pyrosequencing of the 16S rRNA gene) how the archaeal community varies among known LMA (Stylissa carteri, and Stylissa massa), known HMA (Hyrtios erectus and Xestospongia testudinaria) and unknown HMA/LMA status sponge species (Ectyoplasia coccinea, Paratetilla bacca and Petrosia aff. spheroida) collected in a remote location in which very few sponge microbial composition studies have been previously performed (Mayotte, Comores archipelago, France) and comparing the results with those reported in four other geographical areas. Based on archaeal community composition, the known LMA sponges formed a distinct cluster together with Paratetilla bacca, Ectyoplasia coccinea and seawater while the known HMA sponge X. testudinaria formed a cluster with Petrosia aff. spheroida. The known HMA sponge H. erectus, in turn, had an intermediate archaeal community between HMA sponges and sediment samples. In addition to the above, we also showed significant compositional congruence between archaeal and bacterial communities sampled from the same sponge individuals. HMA sponges were mainly dominated by members assigned to the genus Nitrosopumilus while LMA sponges were mainly dominated by members assigned to the genus Cenarchaeum. In general, there was no clear difference in richness between HMA and LMA sponges. Evenness, however, was higher in HMA than LMA sponges. Whilst the present study corroborates some of the traits commonly associated with the HMA-LMA dichotomy (higher evenness in Mayotte HMA sponges), this was not consistent across geographical areas showing that more research is needed to fully understand the HMA/LMA dichotomy as concerns Archaea.

Bacterial composition and putative functions associated with sponges, sediment and seawater from the Tioman coral reef system, Peninsular Malaysia

ABSTRACT Microbial communities associated with sponges play important roles in sponge health, defence and nutrient dynamics in coral reef systems. Here, we used a 16S rRNA gene high-throughput sequencing approach in order to test for differences in bacterial composition and predictive functional differences among two LMA (low microbial abundance) (Stylissa carteri and Stylissa massa), one well-known HMA (high microbial abundance) (Xestospongia testudinaria), one putative HMA (Aaptos lobata) sponge species, sediment and seawater in a coral reef ecosystem surrounding Tioman Island. Our results showed that biotope (sponge species, sediment and seawater) was a significant predictor of composition and abundance of bacterial communities. Proteobacteria was the dominant phylum in S. carteri, seawater, sediment and A. lobata, whilst bacterial communities of S. massa and X. testudinaria were dominated by Cyanobacteria and Chloroflexi, respectively. The predicted metagenome revealed differentially enriched pathways in HMA and LMA sponges. Differentially enriched subcategories in HMA sponges included ‘Signaling Molecules and Interaction’, ‘Carbohydrate Metabolism’ and ‘Excretory System’. Subcategories enriched in LMA sponges included ‘Replication and Repair’, ‘Energy Metabolism’, ‘Metabolism of Cofactors and Vitamins’ and ‘Environmental Adaptation’. Overall, the predicted functional analysis suggests that, although HMA and LMA associated bacterial communities shared core functional features, they use different strategies to defend against pathogens, obtain energy or cope with stress.

Microbial community analysis with a specific statistical approach after a record breaking snowfall in Southern Italy

PurposeSnow and ice ecosystems present unexpectedly high microbial abundance and diversity. Although arctic and alpine snow environments have been intensively investigated from a microbiological point of view, few studies have been conducted in the Apennines. Accordingly, the main purpose of this research was to analyze the microbial communities of the snow collected in two different locations of Capracotta municipality (Southern Italy) after a snowfall record occurred on March 2015 (256 cm of snow in less than 24 h).MethodsBacterial communities were analyzed by the Next-Generation Sequencing techniques. Furthermore, a specific statistical approach for taxonomic hierarchy data was introduced, both for the assessment of diversity within microbial communities and the comparison between different microbiotas. In general, diversity and similarity indices are more informative when computed at the lowest level of the taxonomic hierarchy, the species level. This is not the case with microbial data, for which the species level is not necessarily the most informative. Indeed, the possibility to detect a large number of unclassified records at every level of the hierarchy (even at the top) is very realistic due to both the partial knowledge about the cultivable fraction of microbial communities and limitations to taxonomic assignment connected to the quality and completeness of the 16S rRNA gene reference databases. Thus, a global approach considering information from the whole taxonomic hierarchy was adopted in order to obtain a more consistent assessment of the biodiversity.ResultThe main phyla retrieved in the investigated snow samples were Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Interestingly, DNA from bacteria adapted to thrive at low temperatures, but also from microorganisms normally associated with other habitats, whose presence in the snow could be justified by wind-transport, was found. Biomolecular investigations and statistical data analysis showed relevant differences in terms of biodiversity, composition, and distribution of bacterial species between the studied snow samples.ConclusionThe relevance of this research lies in the expansion of knowledge about microorganisms associated with cold environments in contexts poorly investigated such as the Italian Apennines, and in the development of a global statistical approach for the assessment of biological diversity and similarity of microbial communities as an additional tool to be usefully combined with the barcoding methods.

Diminished rhizosphere and bulk soil microbial abundance and diversity across succession stages in Karst area, southwest China

Soil microorganisms are important for plant nutrients and health. However, our understanding of soil microbial communities in the rhziosphere and bulk soils as plant succession stages increased in the Karst area remains unclear. Here, we evaluated how the bacterial and fungal communities of rhizosphere and bulk soils respond to different vegetation succession stages: grassland (GR), shrubland (SH), secondary forest (SF), and primary forest (PF). The abundance and composition of bacteria and fungi were determined by qPCR and MiSeq high-throughput sequencing methods, respectively. The results showed that the abundance and diversity in rhizosphere and bulk soils were diminished among vegetation succession stages. We found that SOC led to high microbial abundance in GR and SH during the period of primary succession stages, while AP potentially led to low abundance of microbes in the PF and SF of subsequent succession stages. Additionally, the OTUs shared by four succession stages (common OTUs) comprised approximately 87.61 ‐ 98.90% of the total relative abundance of bacteria and fungi in the rhizosphere and bulk soils, which indicated that the composition of fungi and bacteria in these environments were similar across different succession stages. pH might be an important driving factor involved in the similarity of bacterial and fungal compositions among different succession stages. However, the relative abundance of bacterial and fungal phyla across the four vegetation stages was different, and also determined by multiple soil properties. pH was the main factor determining bacterial community structure in rhizosphere soils, whereas SOC was the principal determinant of the same parameter for bacteria in bulk soils, and in both the rhizosphere and bulk soils for fungi. Overall, our results suggested that bacterial and fungal communities in the rhizosphere and bulk soils diminished with vegetation stages, which may provide evidence that mechanisms underlying the soil microbe-driven vegetation succession in the Karst area of southwest China.

Response of ammonia oxidation activities to water-level fluctuations in riparian zones in a column experiment

Biogeochemical hotspots of nitrogen cycling such as ammonia oxidation commonly occur in riparian ecosystems. However, the responses of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to water-level fluctuations (WLF) in riparian zones remain unclear. In this study, two patterns of WLF (gradual waterlogging and drying) were investigated in a 9-month column experiment, and the abundances and activities of AOA and AOB were investigated. The recovery evaluation revealed AOB abundance had not returned to the initial level at the end of the experiment, while AOA abundance had recovered nearly completely. AOA outnumbered AOB at almost all depths, and AOA showed higher resistance and adaptation to WLF than AOB. However, higher microbial abundance was not always linked to the larger contribution to nitrification. Changes in environmental parameters such as moisture and dissolved oxygen caused by WLF instead of ammonia-oxidizing microorganism (AOM) abundance might play a key role in regulating the expression of amoA gene and thus the activity of ammonia oxidizers. In addition, the community structure of AOM evolved over the incubation period. The composition of AOA species in sediment changed in the same way as that in soil, and the Nitrosopumilus cluster showed strong resistance to WLF. Conversely, waterlogging changed the community structure of AOB in soil while drying had no significant effect on the AOB community structure in sediment. This study suggests that the ammonia oxidizers will respond to WLF and eventually affect N fate in riparian ecosystems considering the coupling with other N transformation processes.

Differential processing of dissolved and particulate organic matter by deep-sea sponges and their microbial symbionts

Deep-sea sponges create hotspots of biodiversity and biological activity in the otherwise barren deep-sea. However, it remains elusive how sponge hosts and their microbial symbionts acquire and process food in these food-limited environments. Therefore, we traced the processing (i.e. assimilation and respiration) of 13C- and 15N-enriched dissolved organic matter (DOM) and bacteria by three dominant North Atlantic deep-sea sponges: the high microbial abundance (HMA) demosponge Geodia barretti, the low microbial abundance (LMA) demosponge Hymedesmia paupertas, and the LMA hexactinellid Vazella pourtalesii. We also assessed the assimilation of both food sources into sponge- and bacteria-specific phospholipid-derived fatty acid (PLFA) biomarkers. All sponges were capable of assimilating DOM as well as bacteria. However, processing of the two food sources differed considerably between the tested species: the DOM assimilation-to-respiration efficiency was highest for the HMA sponge, yet uptake rates were 4–5 times lower compared to LMA sponges. In contrast, bacteria were assimilated most efficiently and at the highest rate by the hexactinellid compared to the demosponges. Our results indicate that phylogeny and functional traits (e.g., abundance of microbial symbionts, morphology) influence food preferences and diet composition of sponges, which further helps to understand their role as key ecosystem engineers of deep-sea habitats.