Soil-foraging animals alter the composition and co-occurrence of microbial communities in a desert shrubland

Meta-analysis reveals that vertebrates enhance plant litter decomposition at the global scale

Evidence is mounting that vertebrate defaunation greatly impacts global biogeochemical cycling. Yet, there is no comprehensive assessment of the potential vertebrate influence over plant decomposition, despite litter decay being one of the largest global carbon fluxes. We therefore conducted a global meta-analysis to evaluate vertebrate effects on litter mass loss and associated element release across terrestrial and aquatic ecosystems. Here we show that vertebrates affected litter decomposition by various direct and indirect pathways, increasing litter mass loss by 6.7% on average, and up to 34.4% via physical breakdown. This positive vertebrate impact on litter mass loss was consistent across contrasting litter types (woody and non-woody), climatic regions (boreal, temperate and tropical), ecosystem types (aquatic and terrestrial) and vertebrate taxa, but disappeared when evaluating litter nitrogen and phosphorus release. Moreover, we found evidence of interactive effects between vertebrates and non-vertebrate decomposers on litter mass loss, and a larger influence of vertebrates at mid-to-late decomposition stages, contrasting with the invertebrate effect known to be strongest at early decomposition stage. Our synthesis demonstrates a global vertebrate control over litter mass loss, and further stresses the need to account for vertebrates when assessing the impacts of biodiversity loss on biogeochemical cycles.

Responses of soil greenhouse gas emissions to soil mesofauna invasions and its driving mechanisms in the alpine tundra: A microcosm study

Climate change is resulting in significant modifications of the altitudinal patterns of soil fauna in mountains, leading to their upward invasion and alteration of soil ecological processes. However, the effects of soil greenhouse gas (GHG) emissions from soil mesofauna invasion and their driving mechanisms have not been clearly understood. To address this knowledge gap, we simulated a soil mesofauna invasion from an Erman's birch forest (EB) to the alpine tundra (AT) of the Changbai Mountain in Northeast China. Four treatments were established: no soil mesofauna (S0), native species (SN), invasive species (SI), and invasive species superposed native species (SS). We conducted a 79-day microcosm experiment, utilizing gas chromatography and high-throughput sequencing, to explore the variations in soil greenhouse gas emissions and their driving factors. Results showed that the cumulative CO2 emissions under SN, SI, and SS, compared with S0, increased by 34.13 %, 73.93 %, and 107.64 % and cumulative N2O emissions increased by 59.05 %, 101.18 %, and 183.88 %, respectively. Compared to SN, the cumulative emissions of CO2 and N2O increased by 29.89 % and 26.31 % under SI and by 54.91 % and 78.59 % under SS, respectively. The impacts of invasive species and native species on greenhouse gases were not a simple additive effect. Abiotic (soil variables) and biotic (soil mesofauna and microbial diversity) factors explained 37.76 % and 44.41 % of the total variations in CO2 and N2O emissions, respectively, in which NH4+-N and C: N ratios contributed the largest variations. The contribution of soil mesofauna diversity to the variations in CO2 and N2O emissions was higher than that of microbial diversity. The bacterial network graph density was correlated with soil CO2 and N2O emissions. Our findings highlight that soil mesofauna invasions increased GHG emissions, and these variations were predominantly explained by biotic rather than abiotic factors.

Earthworms synergize with indigenous soil functional microorganisms to accelerate the preferential degradation of the highly toxic S-enantiomer of the fungicide imazalil in soil

The roles of soil and earthworm gut microorganisms in the degradation of the chiral fungicide imazalil (IMA) enantiomers were systemically studied in soil-earthworm systems. S-IMA degraded slower than R-IMA in soil without earthworms. After the addition of earthworms, S-IMA degraded faster than R-IMA. Methylibium was the potential degradative bacterium likely related to the preferential degradation of R-IMA in soil. However, the addition of earthworms significantly decreased the relative abundance of Methylibium, especially in R-IMA-treated soil. Meanwhile, a new potential degradative bacterium Aeromonas first appeared in soil-earthworm systems. Compared with enantiomer-treated soil, the relative abundance of indigenous soil bacterium Kaistobacter significantly boomed in enantiomer-treated soil with earthworms. Interestingly, Kaistobacter in the earthworm gut also obviously increased after exposure to enantiomers, particularly in S-IMA-treated soil, which was associated with the significant increase in Kaistobacter in soil. More importantly, the relative abundances of Aeromonas and Kaistobacter in S-IMA-treated soil were obviously higher than those in R-IMA-treated soil after the addition of earthworms. Moreover, these two potential degradative bacteria were also potential bacterial hosts of the biodegradation genes p450 and bph. Collectively, gut microorganisms are important helpers in soil pollution remediation by participating in the preferential degradation of S-IMA mediated by indigenous soil microorganisms.

The reciprocal changes in dominant species with complete metabolic functions explain the decoupling phenomenon of microbial taxonomic and functional composition in a grassland

The decoupling of microbial functional and taxonomic components refers to the phenomenon that a drastic change in microbial taxonomic composition leads to no or only a gentle change in functional composition. Although many studies have identified this phenomenon, the mechanisms underlying it are still unclear. Here we demonstrate, using metagenomics data from a steppe grassland soil under different grazing and phosphorus addition treatments, that there is no “decoupling” in the variation of taxonomic and metabolic functional composition of the microbial community within functional groups at species level. In contrast, the high consistency and complementarity between the abundance and functional gene diversity of two dominant species made metabolic functions unaffected by grazing and phosphorus addition. This complementarity between the two dominant species shapes a bistability pattern that differs from functional redundancy in that only two species cannot form observable redundancy in a large microbial community. In other words, the “monopoly” of metabolic functions by the two most abundant species leads to the disappearance of functional redundancy. Our findings imply that for soil microbial communities, the impact of species identity on metabolic functions is much greater than that of species diversity, and it is more important to monitor the dynamics of key dominant microorganisms for accurately predicting the changes in the metabolic functions of the ecosystems.

Bioturbation by echidna (

Bioturbation by digging animals is important for key forest ecosystem processes such as soil turnover, decomposition, nutrient cycling, water infiltration, seedling recruitment, and fungal dispersal. Despite their widespread geographic range, little is known about the role of the short-beaked echidna (Tachyglossus aculeatus) in forest ecosystems. We measured the density and size of echidna diggings in the Northern Jarrah Forest, south-western Australia, to quantify the contribution echidna make to soil turnover. We recorded an overall density of 298 echidna diggings per hectare, 21% of which were estimated to be less than 1 month old. The average size of digs was 50 ± 25 mm in depth and 160 ± 61 mm in length. After taking into account seasonal digging rates, we estimated that echidnas turn over 1.23 tonnes of soil ha−1 year−1 in this forest, representing an important role in ecosystem dynamics. Our work contributes to the growing body of evidence quantifying the role of these digging animals as critical ecosystem engineers. Given that the echidna is the only Australian digging mammal not severely impacted by population decline or range reduction, its functional contribution to health and resilience of forest ecosystems is increasingly important due to the functional loss of most Australian digging mammals.

Animal Activities of the Key Herbivore Plateau Pika (Ochotona curzoniae) on the Qinghai-Tibetan Plateau Affect Grassland Microbial Networks and Ecosystem Functions

Plateau pikas (Ochotona curzoniae) are high-altitude model animals and famous "ecosystem engineers" on the Qinghai-Tibet Plateau. Pika activities may accelerate the degradation of alpine meadows. Nevertheless, little is known about the responses of bacterial, fungal, and archaeal communities, and ecosystem multifunctionality to pika perturbations. To address this question, we studied the impacts of only pika disturbance and combined disturbance (pika disturbance and grazing) on ecological networks of soil microbial communities and ecosystem multifunctionality. Our results demonstrated that Proteobacteria, Ascomycota, and Crenarchaeota were dominant in bacteria, fungi, and archaea, respectively. Bacteria, fungi, and archaea were all influenced by the combined disturbance of grazing and pika. Most fungal communities became convergent, while bacterial and archaeal communities became differentiated during the succession of surface types. In particular, the bacterial and fungal networks were less stable than archaeal networks. In response to the interference, cross-domain cooperation between bacterial and fungal communities increased, while competitive interactions between bacterial and archaeal communities increased. Pika disturbance at high intensity significantly reduced the ecosystem multifunctionality. However, the mixed effects of grazing and pika weakened such influences. This study revealed how pika activities affected microbial networks and ecosystem multifunctionality. These results provide insights to designing reasonable ecological management strategies for alpine grassland ecosystems.

Biochar Amendment and Nitrogen Fertilizer Contribute to the Changes in Soil Properties and Microbial Communities in a Paddy Field

Biochar amendment can influence the abundance, activity, and community structure of soil microbes. However, scare information is present about the effect of the combined application of biochar with synthetic nitrogen (N) fertilizer under paddy field condition. We aimed to resolve this research gap in rice field conditions through different biochar in combination with N fertilizers on soil nutrients, soil microbial communities, and rice grain yield. The present study involves eight treatments in the form of biochar (0, 10, 20, and 30 t ha-1) and N (135 and 180 kg ha-1) fertilizer amendments. The soil microbial communities were characterized using high-throughput sequencing of 16S and Internal transcribed spacer (ITS) ribosomal RNA gene amplicons. Experiential findings showed that the treatments had biochar amendments along with N fertilizer significantly advanced soil pH, soil organic carbon (SOC), total nitrogen (TN), soil microbial carbon (SMBC), soil microbial nitrogen (SMBN), and rice grain yield in comparison to sole N application. Furthermore, in comparison with control in the first year (2019), biochar amendment mixed with N fertilizer had more desirable relative abundance of microorganism, phyla Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia with better relative abundance ranging from 8.49, 4.60, 46.30, and 1.51% in T7, respectively. Similarly, during 2020, bacteria phyla Acidobacteria, Actinobacteria, Bacteroidetes, Gemmatimonadetes, Planctomycetes, and Verrucomicrobia were resulted in higher and ranging from 8.69, 5.18, 3.5, 1.9, 4.0, and 1.6%, in biochar applied treatments, respectively, as compared to control (T1). Among the treatments, Sphingopyxis and Thiobacillus bacterial genus were in higher proportion in T7 and T3, respectively, as compared to other treatments and Bacillus was higher in T6. Interestingly, biochar addition significantly decreased the soil fungi phyla Ascomycota, Basidiomycota, Chytridiomycota, and Rozellomycota, in 2020 as compared to 2019. Whereas biochar addition to soil decreased Echria, Kohlmeyeriopsis, and Westerdykella fungal genus as compared to non-biochar treatments. The redundancy analysis showed that soil biochemical traits were positively correlated with soil bacteria. In addition, correlation analysis showed that soil bacteria including Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, and Proteobacteria strongly correlated with rice grain yield. This study demonstrated that soil nutrients and bacteria contribute to an increase in rice yield in combined biochar amendment with lower N treatments.

Diversity and structure of the microbial community in rhizosphere soil of Fritillaria ussuriensis at different health levels

Fritillaria wilt is a kind of soil-borne disease that causes a large reduction in the yield of Fritillaria ussuriensis. The diversity and structure of the soil microbial community are important factors affecting the health of Fritillaria ussuriensis. The analysis of the microbial community in the diseased and healthy soils provided a theoretical basis for revealing the pathological mechanism and prevention of Fritillaria wilt disease. In the present study, we sequenced the soil microorganisms from healthy (H), pathology (P) and blank (B) soil samples by Illumina MiSeq. Determined the soil physicochemical properties respectively, analyzed the soil microbial diversity and structure, and constructed single factor co-correlation networks among microbial genera. The results showed that Ascomycota (48.36%), Mortierellomycota (23.06%), Basidiomycota (19.00%), Proteobacteria (31.74%), and Acidobacteria (20.95%) were dominant in the soil. The diversity of healthy soil was significantly greater than that of diseased soil samples (P and B) (P < 0.05). The populations of Fusarium and Humicola significantly increased in the diseased soil sample (P and B) (P < 0.05). RB41 (4.74%) and Arthrobacter (3.30%) were the most abundant genera in the healthy soil. Total nitrogen (TN), available nitrogen (AN), total potassium (TK), available potassium (AK), and inorganic salt (salt) were significantly correlated with soil microbial communities (P < 0.05). The relationship between fungi and the plant was mostly positive, whereas bacteria showed the opposite trend. In conclusion, the diversity and structure of the soil microbial community were closely related to the health level of Fritillaria ussuriensis. Fusarium and Humicola affect the severity of Fritillaria wilt disease, while RB41 and Arthrobacter are the important indicators for maintaining the health of Fritillaria ussuriensis. Moreover, environmental factors greatly affect the abundance and formation of soil microbial community. The interactions in microbial communities also influence the healthy growth of Fritillaria ussuriensis.

Mussels and Local Conditions Interact to Influence Microbial Communities in Mussel Beds

Microbiomes are increasingly recognized as widespread regulators of function from individual organism to ecosystem scales. However, the manner in which animals influence the structure and function of environmental microbiomes has received considerably less attention. Using a comparative field study, we investigated the relationship between freshwater mussel microbiomes and environmental microbiomes. We used two focal species of unionid mussels, Amblema plicata and Actinonaias ligamentina, with distinct behavioral and physiological characteristics. Mussel microbiomes, those of the shell and biodeposits, were less diverse than both surface and subsurface sediment microbiomes. Mussel abundance was a significant predictor of sediment microbial community composition, but mussel species richness was not. Our data suggest that local habitat conditions which change dynamically along streams, such as discharge, water turnover, and canopy cover, work in tandem to influence environmental microbial community assemblages at discreet rather than landscape scales. Further, mussel burrowing activity and mussel shells may provide habitat for microbial communities critical to nutrient cycling in these systems.

Grass waste utilization to alter aggregate-related carbon chemical composition and fungal community structure in apple orchard

The grass-waste management model affects soil organic carbon (SOC) and the microorganism community structure; however, studies on the relationship between the fungal community structure and the SOC chemical component at the aggregate level are poor. Solid-state ¹³C NMR and 18 S rDNA methods were used to evaluate the relationship between the SOC chemical composition and fungal community abundance at the aggregate level. Grass mulching significantly increased the percentage of labile carbon O-alkyl C (5.19%-11.79%) and decreased the instability of SOC (1.38-0.69). Microaggregates contained higher alkyl C (33.77%) and lower aromatic C (18.31%), and the A/O-A ratio (1.03) was higher than that of macroaggregates (0.89-0.96). Ascomycota, Basidiomycota and Mortierellomycota dominated the fungal community at the phylum level, and their abundance increased after grass mulching. Microaggregates supported more microbial diversity and richness and were rich in the Ascomycota (36.69%-67.49%) phylum, while LM aggregates were rich in Basidiomycota (5.62%-39.84%). We proved that changes in the O-alkyl C, carbonyl C, aromatic C and alkyl C of SOC chemical components were closely connected to fungal community composition, which together explained the change in fungal composition by 63.81%-71.99% among aggregates. We concluded that alterations in the chemical form of organic carbon were closely related to a change in the soil fungal community. This connection has a positive impact on soil nutrient utilization and SOC conversion in fruit-grass composite ecosystems and promotes the understanding of the relationship between the soil microbial community and nutrient cycling during long-term grass waste utilization.

Earthworms accelerated the degradation of the highly toxic acetochlor S-enantiomer by stimulating soil microbiota in repeatedly treated soils

This study investigated the effects of earthworms on the enantioselective degradation of chloroacetamide herbicide acetochlor with soil microorganisms in repeatedly treated soils. The S-enantiomer degraded more slowly and exerted stronger inhibition on soil microbial functions than the R-enantiomer in single soil system. A synergistic effect was observed between soil microorganisms and earthworms that accelerated the degradation of both the enantiomers, particularly the highly toxic S-enantiomer, which resulted in the preferential degradation of S-enantiomer in soil-earthworm system. Earthworms stimulated five potential indigenous degraders (i.e. Lysobacter, Kaistobacter, Flavobacterium, Arenimonas, and Aquicell), induced two new potential degraders (i.e. Aeromonas and Algoriphagus), and also significantly strengthened the correlations among these seven dominant potential degraders and other microorganisms. Notably, the relative abundances of Flavobacterium and Aeromonas in soil treated with earthworms for S-enantiomer were higher than those for R-enantiomer. Furthermore, earthworms significantly stimulated overall soil microbial activity and improved three microbial metabolic pathways, and xenobiotics biodegradation and metabolism, signal transduction, cell motility, particularly for the S-enantiomer treatment with earthworms, which alleviated the strong inhibition of S-enantiomer on microbial community functions. This study confirmed that earthworms accelerated the degradation of the highly toxic acetochlor S-enantiomer in soil, providing a potential approach in chloroacetamide herbicide-polluted soil remediation.

Fungal Endophytic Community and Diversity Associated with Desert Shrubs Driven by Plant Identity and Organ Differentiation in Extremely Arid Desert Ecosystem

Despite desert ecosystem being crucial to our understanding of natural geography, species evolution and global climate change, there is limited information on the dynamics of their composition and the diversity of endophytic fungi communities driven by plant identity and organ differentiation. Here, an extensive investigation of endophytic fungal microbiome in root, stem, and leaf organs associated with five xerophyte shrubs in an extremely arid desert, Northwest China, were examined. The fungal community dominated by Dothideomycetes and Pleosporales. Shrub species strongly drive the niche-based processes of endophytic fungi across the root, stem and leaf compartments. The diversity and composition of endophytic fungi in stem showed higher variability among plant species than leaf and root. The fungal communities in root libraries were more diverse and exhibited a remarkable differentiation of community composition. We further demonstrated the significant host preferences and tissue specificity of desert endophytic fungi, and unique specific taxa were also observed. The co-occurrence network revealed the coexistence of fungal endophytes in arid desert, and the root fungal network harbored the highest interspecies connectivity. Members of Pleosporales were the most common keystone species in the root fungal network. This is the first report of mycobiota in both plant species and organ differentiation in an extremely arid desert ecosystem.

Foraging by an avian ecosystem engineer extensively modifies the litter and soil layer in forest ecosystems

Ecosystem engineers physically modify their environment, thereby altering habitats for other organisms. Increasingly, "engineers" are recognized as an important focus for conservation and ecological restoration because their actions affect a range of ecosystem processes and thereby influence how ecosystems function. The Superb Lyrebird Menura novaehollandiae is proposed as an ecosystem engineer in forests of southeastern Australia due to the volume of soil and litter it turns over when foraging. We measured the seasonal and spatial patterns of foraging by Lyrebirds and the amount of soil displaced in forests in the Central Highlands, Victoria. We tested the effects of foraging on litter, soil nutrients and soil physical properties by using an experimental approach with three treatments: Lyrebird exclusion, Lyrebird exclusion with simulated foraging, and non-exclusion reference plots. Treatments were replicated in three forest types in each of three forest blocks. Lyrebirds foraged extensively in all forest types in all seasons. On average, Lyrebirds displaced 155.7 Mg/ha of litter and soil in a 12-month period. Greater displacement occurred where vegetation complexity (<50 cm height) was low. After two years of Lyrebird exclusion, soil compaction (top 7.5 cm) increased by 37% in exclusion plots compared with baseline measures, while in unfenced plots it decreased by 22%. Litter depth was almost three times greater in fenced than unfenced plots. Soil moisture, pH, and soil nutrients showed no difference between treatments. The enormous extent of litter and soil turned over by the Superb Lyrebird is unparalleled by any other vertebrate soil engineer in terrestrial ecosystems globally. The profound influence of such foraging activity on forest ecosystems is magnified by its year-round pattern and widespread distribution. The disturbance regime that Lyrebirds impose has implications for diverse ecosystem processes including decomposition and nutrient cycling, the composition of litter- and soil-dwelling invertebrate communities, the shaping of ground-layer vegetation patterns, and fire behavior and post-fire ecosystem recovery. Maintaining Lyrebird populations as a key facilitator of ecosystem function is now timely and critical as unprecedented wildfires in eastern Australia in summer 2019-2020 have severely burned ~12 million ha of forest, including ~30% of the geographic range of the Superb Lyrebird.

Changes in microbial community structure due to chronic trace element concentrations in different sizes of soil aggregates

Studies on the effects of trace elements (TEs) (e.g. Cu, Cd, Zn) on soil microbial communities have provided useful information on the toxicity of TEs to microbes. However, previous studies mainly focused on the effects of TEs on microbial community structure in intact soil, while there are few studies on the impact of TEs on microbial community structure in soil aggregates. In this study, soils previously polluted for 20 years, and now containing low and high TE concentrations derived from, now abandoned, metal smelters were sampled from the surface layer (0-15 cm) of two adjacent Chinese paddy fields. The aim was to determine the effects of TEs on the soil microbial biomass and community structure in different sized soil aggregates. Long-term high TE pollution decreased microbial biomass concentration and species, changed the proportion of bacteria and fungi and decreased the diversity of bacteria in the different sized aggregates. The microbial communities in soil aggregates became clustered with increasing TE concentrations.

Uncovering Unique Green Algae and Cyanobacteria Isolated from Biocrusts in Highly Saline Potash Tailing Pile Habitats, Using an Integrative Approach

Potash tailing piles caused by fertilizer production shape their surroundings because of the associated salt impact. A previous study in these environments addressed the functional community "biocrust" comprising various micro- and macro-organisms inhabiting the soil surface. In that previous study, biocrust microalgae and cyanobacteria were isolated and morphologically identified amongst an ecological discussion. However, morphological species identification maybe is difficult because of phenotypic plasticity, which might lead to misidentifications. The present study revisited the earlier species list using an integrative approach, including molecular methods. Seventy-six strains were sequenced using the markers small subunit (SSU) rRNA gene and internal transcribed spacer (ITS). Phylogenetic analyses confirmed some morphologically identified species. However, several other strains could only be identified at the genus level. This indicates a high proportion of possibly unknown taxa, underlined by the low congruence of the previous morphological identifications to our results. In general, the integrative approach resulted in more precise species identifications and should be considered as an extension of the previous morphological species list. The majority of taxa found were common in saline habitats, whereas some were more likely to occur in nonsaline environments. Consequently, biocrusts in saline environments of potash tailing piles contain unique microalgae and cyanobacteria that will possibly reveal several new taxa in more detailed future studies and, hence, provide new data on the biodiversity, as well as new candidates for applied research.

Bacterial Operational Taxonomic Units Replace the Interactive Roles of Other Operational Taxonomic Units Under Strong Environmental Changes

Background

Microorganisms are an important component of an aquatic ecosystem and play a critical role in the biogeochemical cycle which influences the circulation of the materials and maintains the balance in aquatic ecosystems.

Objective

The seasonal variation along with the impact of anthropogenic activities, water quality, bacterial community composition and dynamics in the Loktak Lake, the largest freshwater lake of North East India, located in the Indo-Burma hotspot region was assessed during post-monsoon and winter season through metagenome analysis.

Methods

Five soil samples were collected during Post-monsoon and winter season from the Loktak Lake that had undergone different anthropogenic impacts. The metagenomic DNA of the soil samples was extracted using commercial metagenomic DNA extraction kits following the manufacturer’s instruction. The extracted DNA was used to prepare the NGS library and sequenced in the Illumina MiSeq platform.

Results

Metagenomics analysis reveals Proteobacteria as the predominant community followed by Acidobacteria and Actinobacteria. The presence of these groups of bacteria indicates nitrogen fixation, oxidation of iron, sulfur, methane, and source of novel antibiotic candidates. The bacterial members belonging to different groups were involved in various biogeochemical processes, including fixation of carbon and nitrogen, producing streptomycin, gramicidin and perform oxidation of sulfur, sulfide, ammonia, and methane.

Conclusion

The outcome of this study provides a valuable dataset representing a seasonal profile across various land use and analysis, targeting at establishing an understanding of how the microbial communities vary across the land use and the role of keystone taxa. The findings may contribute to searches for microbial bio-indicators as biodiversity markers for improving the aquatic ecosystem of the Loktak Lake.

Multifunctionality of biocrusts is positively predicted by network topologies consistent with interspecies facilitation

The potential of biodiversity loss to impair the delivery of ecosystem services has motived ecologists to better understand the relationship between biodiversity and ecosystem functioning. Although increasing evidence underlines the collective contribution of different biodiversity components on the simultaneous performance of multiple functions (multifunctionality), we know little about the trade‐offs between individual diversity effects and the extent to which they determine multifunctionality differentially. Here, at a subcontinental scale of 62 dryland sites, we show in phototrophic microbiota of biological soil crusts (biocrusts) that, whereas richness alone is unable to guarantee the maxima of multifunctional performance, interspecies facilitation and compositional identity are particularly stronger but often neglected predictors. The inconsistent effects of different biodiversity components imply that soil multifunctionality can be lost despite certain species remaining present. Moreover, we reveal a significant empirical association between species functional importance and its topological feature in co‐occurrence networks, indicating a functional signal of species interaction. Nevertheless, abundant species tend to isolate and merely interact within small topological structures, but rare species were tightly connected in complicated network modules. Our findings suggest that abundant and rare species of soil phototrophs exhibit distinct functional relevance. These results give a comprehensive view of how soil constructive species drive multifunctionality in biocrusts and ultimately promote a deeper understanding of the consequences of biodiversity loss in real‐world ecosystems.

Digging mammal reintroductions reduce termite biomass and alter assemblage composition along an aridity gradient

Invasions can trigger cascades in ecological communities by altering species interactions. Following the introduction of cats and foxes into Australia, one tenth of Australia's terrestrial mammal species became extinct, due to predation, while many continue to decline. The broader consequences for Australian ecosystems are poorly understood. Soil-dwelling invertebrates are likely to be affected by the loss of fossorial native mammals, which are predators and disturbance agents. Using reintroductions as a model for ecosystems prior to species loss, we tested the hypothesis that mammal reintroduction leads to reduced vegetation cover and altered termite assemblages, including declines in abundance and biomass and changed species composition. We hypothesised that the magnitude of mammal reintroduction effects would diminish with increasing aridity, which affects resource availability. We compared six paired sites inside and outside three reintroduction sanctuaries across an aridity gradient. We sampled termite assemblages using soil trenches and measured habitat availability. Reintroductions were associated with increased bare ground and reduced vegetation, compared with controls. Aridity also had an underlying influence on vegetation cover by limiting water availability. Termite abundance and biomass were lower where mammals were reintroduced and the magnitude of this effect decreased with increasing aridity. Termite abundance was highest under wood, and soil-nesting wood-feeders were most affected inside sanctuaries. Ecological cascades resulting from exotic predator invasions are thus likely to have increased termite biomass and altered termite assemblages, but impacts may be lower in less-productive habitats. Our findings have implications for reserve carrying capacities and understanding of assemblage reconstruction following ecological cascades.

Effects of digging by a native and introduced ecosystem engineer on soil physical and chemical properties in temperate grassy woodland

Temperate grasslands and woodlands are the focus of extensive restoration efforts worldwide. Reintroduction of locally extinct soil-foraging and burrowing animals has been suggested as a means to restore soil function in these ecosystems. Yet little is known about the physical and chemical effects of digging on soil over time and how these effects differ between species of digging animal, vegetation types or ecosystems. We compared foraging pits of a native reintroduced marsupial, the eastern bettong (Bettongia gaimardi) and that of the exotic European rabbit (Oryctolagus cuniculus). We simulated pits of these animals and measured pit dimensions and soil chemical properties over a period of 2 years. We showed that bettong and rabbit pits differed in their morphology and longevity, and that pits had a strong moderating effect on soil surface temperatures. Over 75% of the simulated pits were still visible after 2 years, and bettong pits infilled faster than rabbit pits. Bettong pits reduced diurnal temperature range by up to 25 °C compared to the soil surface. We did not find any effects of digging on soil chemistry that were consistent across vegetation types, between bettong and rabbit pits, and with time since digging, which is contrary to studies conducted in arid biomes. Our findings show that animal foraging pits in temperate ecosystems cause physical alteration of the soil surface and microclimatic conditions rather than nutrient changes often observed in arid areas.

Soil biological responses to, and feedbacks on, trophic rewilding

Trophic rewilding-the (re)introduction of missing large herbivores and/or their predators-is increasingly proposed to restore biodiversity and biotic interactions, but its effects on soils have been largely neglected. The high diversity of soil organisms and the ecological functions they perform mean that the full impact of rewilding on ecosystems cannot be assessed considering only above-ground food webs. Here we outline current understanding on how animal species of rewilding interest affect soil structure, processes and communities, and how in turn soil biota may affect species above ground. We highlight considerable uncertainty in soil responses to and feedbacks on above-ground consumers, with potentially large implications for rewilding interactions with global change. For example, the impact of large herbivores on soil decomposers and plant-soil interactions could lead to reduced carbon sequestration, whereas herbivore interactions with keystone biota such as mycorrhizal fungi, dung beetles and bioturbators could promote native plants and ecosystem heterogeneity. Moreover, (re)inoculation of keystone soil biota could be considered as a strategy to meet some of the objectives of trophic rewilding. Overall, we call for the rewilding research community to engage more with soil ecology experts and consider above-ground-below-ground linkages as integral to assess potential benefits as well as pitfalls.This article is part of the theme issue 'Trophic rewilding: consequences for ecosystems under global change'.

Bacterial Biomarkers of Marcellus Shale Activity in Pennsylvania

Unconventional oil and gas (UOG) extraction, also known as hydraulic fracturing, is becoming more prevalent with the increasing use and demand for natural gas; however, the full extent of its environmental impacts is still unknown. Here we measured physicochemical properties and bacterial community composition of sediment samples taken from twenty-eight streams within the Marcellus shale formation in northeastern Pennsylvania differentially impacted by hydraulic fracturing activities. Fourteen of the streams were classified as UOG+, and thirteen were classified as UOG- based on the presence of UOG extraction in their respective watersheds. One stream was located in a watershed that previously had UOG extraction activities but was recently abandoned. We utilized high-throughput sequencing of the 16S rRNA gene to infer differences in sediment aquatic bacterial community structure between UOG+ and UOG- streams, as well as correlate bacterial community structure to physicochemical water parameters. Although overall alpha and beta diversity differences were not observed, there were a plethora of significantly enriched operational taxonomic units (OTUs) within UOG+ and UOG- samples. Our biomarker analysis revealed many of the bacterial taxa enriched in UOG+ streams can live in saline conditions, such as Rubrobacteraceae. In addition, several bacterial taxa capable of hydrocarbon degradation were also enriched in UOG+ samples, including Oceanospirillaceae. Methanotrophic taxa, such as Methylococcales, were significantly enriched as well. Several taxa that were identified as enriched in these samples were enriched in samples taken from different streams in 2014; moreover, partial least squares discriminant analysis (PLS-DA) revealed clustering between streams from the different studies based on the presence of hydraulic fracturing along the second axis. This study revealed significant differences between bacterial assemblages within stream sediments of UOG+ and UOG- streams and identified several potential biomarkers for evaluating and monitoring the response of autochthonous bacterial communities to potential hydraulic fracturing impacts.

Cyanobacterial Community Composition and Bacteria-Bacteria Interactions Promote the Stable Occurrence of Particle-Associated Bacteria

Within meso/eutrophic freshwater ecosystems the dominance of cyanobacterial blooms during summer months has substantial impacts on ecosystem function with the production of toxins and subsequent induction of hypoxia altering food web structures and biogeochemical cycles. Cyanobacterial aggregates are extensively colonized by heterotrophic bacteria that provide the cyanobacteria with key nutrients and contribute towards remineralisation of organic matter. Here we sampled from five sites within a shallow eutrophic pond over a 6 months period, relating changes in the abundance of particle-associated heterotrophic taxa to phytoplankton abundance, toxin gene copies and physiochemical properties. The abundance of a majority of particle-associated bacteria were stable, in that they persisted despite perturbation. Cyanobacterial species abundance more likely correlated with stable rather than unstable bacteria and unstable bacteria were associated with allochthonous (terrestrial) organic matter. The occurrence of the most stable bacteria was correlated with large numbers of other bacteria suggesting bacteria-bacteria interactions have implications for the stable occurrence of microorganisms on particles. Freshwater ecosystems are frequently inundated with fresh nutrients in the form of surface runoff and experience an increasing number of high temperature days. In addition to increasing the severity and longevity of cyanobacterial blooms, run-off changes the nature of the particle-associated community compromising stability. This disruption has the potential to drive changes in the carbon and nitrogen cycles and requires further attention.

Gut region influences the diversity and interactions of bacterial communities in pikas (Ochotona curzoniae and Ochotona daurica)

The mammalian microbial communities in the gastrointestinal tract (GIT) play important roles in host nutrition and health. However, we still lack an understanding of how these communities are organized across GIT in natural environments. Here, using 16S rRNA gene sequencing, we analyzed the bacterial community diversity, network interactions and ecosystem stability across five gut regions (mouth, stomach, small intestine, cecum and colon) emanating from two common pika species in China, including Plateau pikas (Ochotona curzoniae) inhabiting high-altitude regions, as well as Daurian pikas (O. daurica) occupying low-altitude areas. The relative abundances of dominant Bacteroidetes and Firmicutes exhibited an increasing trend from mouth to colon. Cecum and colon harbored higher bacterial diversity compared with other anatomical regions. Gut region significantly influenced the structure of bacterial communities in the GIT. Network analysis indicated that topological features showed marked variations among gut regions. Interestingly, the ecosystem stability of bacterial communities increased gradually from mouth to colon. Our results suggest that gut region influences the diversity, structure and network interactions of bacterial communities in pikas. For hindgut-fermenting herbivorous mammals, relatively higher bacterial diversity and ecosystem stability in the cecum may provide a favorable condition for the fermentation of indigestible plant polysaccharides.

A global database and "state of the field" review of research into ecosystem engineering by land animals

Ecosystem engineers have been widely studied for terrestrial systems, but global trends in research encompassing the range of taxa and functions have not previously been synthesised. We reviewed contemporary understanding of engineer fauna in terrestrial habitats and assessed the methods used to document patterns and processes, asking: (a) which species act as ecosystem engineers and with whom do they interact? (b) What are the impacts of ecosystem engineers in terrestrial habitats and how are they distributed? (c) What are the primary methods used to examine engineer effects and how have these developed over time? We considered the strengths, weaknesses and gaps in knowledge related to each of these questions and suggested a conceptual framework to delineate "significant impacts" of engineering interactions for all terrestrial animals. We collected peer-reviewed publications examining ecosystem engineer impacts and created a database of engineer species to assess experimental approaches and any additional covariates that influenced the magnitude of engineer impacts. One hundred and twenty-two species from 28 orders were identified as ecosystem engineers, performing five ecological functions. Burrowing mammals were the most researched group (27%). Half of all studies occurred in dry/arid habitats. Mensurative studies comparing sites with and without engineers (80%) were more common than manipulative studies (20%). These provided a broad framework for predicting engineer impacts upon abundance and species diversity. However, the roles of confounding factors, processes driving these patterns and the consequences of experimentally adjusting variables, such as engineer density, have been neglected. True spatial and temporal replication has also been limited, particularly for emerging studies of engineer reintroductions. Climate change and habitat modification will challenge the roles that engineers play in regulating ecosystems, and these will become important avenues for future research. We recommend future studies include simulation of engineer effects and experimental manipulation of engineer densities to determine the potential for ecological cascades through trophic and engineering pathways due to functional decline. We also recommend improving knowledge of long-term engineering effects and replication of engineer reintroductions across landscapes to better understand how large-scale ecological gradients alter the magnitude of engineering impacts.

Temperature regulates deterministic processes and the succession of microbial interactions in anaerobic digestion process

Temperature plays crucial roles in microbial interactions that affect the stability and performance of anaerobic digestion. In this study, the microbial interactions and their succession in the anaerobic digestion process were investigated at three levels, represented by (1) present and (2) active micro-organisms, and (3) gene expressions under a temperature gradient from 25 to 55 °C. Network topological features indicated a global variation in microbial interactions at different temperatures. The variations of microbial interactions in terms of network modularity and deterministic processes based on topological features, corresponded well with the variations of methane productions, but not with temperatures. A common successional pattern of microbial interactions was observed at different temperatures, which showed that both deterministic processes and network modularity increased over time during the digestion process. It was concluded that the increase in temperature-mediated network modularity and deterministic processes on shaping the microbial interactions improved the stability and efficiency of anaerobic digestion process.

Strategies for managing rival bacterial communities: Lessons from burying beetles

The role of bacteria in animal development, ecology and evolution is increasingly well understood, yet little is known of how animal behaviour affects bacterial communities. Animals that benefit from defending a key resource from microbial competitors are likely to evolve behaviours to control or manipulate the animal's associated external microbiota. We describe four possible mechanisms by which animals could gain a competitive edge by disrupting a rival bacterial community: "weeding," "seeding," "replanting" and "preserving." By combining detailed behavioural observations with molecular and bioinformatic analyses, we then test which of these mechanisms best explains how burying beetles, Nicrophorus vespilloides, manipulate the bacterial communities on their carcass breeding resource. Burying beetles are a suitable species to study how animals manage external microbiota because reproduction revolves around a small vertebrate carcass. Parents shave a carcass and apply antimicrobial exudates on its surface, shaping it into an edible nest for their offspring. We compared bacterial communities in mice carcasses that were either fresh, prepared by beetles or unprepared but buried underground for the same length of time. We also analysed bacterial communities in the burying beetle's gut, during and after breeding, to understand whether beetles could be "seeding" the carcass with particular microbes. We show that burying beetles do not "preserve" the carcass by reducing bacterial load, as is commonly supposed. Instead, our results suggest they "seed" the carcass with bacterial groups which are part of the Nicrophorus core microbiome. They may also "replant" other bacteria from the carcass gut onto the surface of their carrion nest. Both these processes may lead to the observed increase in bacterial load on the carcass surface in the presence of beetles. Beetles may also "weed" the bacterial community by eliminating some groups of bacteria on the carcass, perhaps through the production of antimicrobials themselves. Whether these alterations to the bacterial community are adaptive from the beetle's perspective, or are simply a by-product of the way in which the beetles prepare the carcass for reproduction, remains to be determined in future work. In general, our work suggests that animals might use more sophisticated techniques for attacking and disrupting rival microbial communities than is currently appreciated.

Not just browsing: an animal that grazes phyllosphere microbes facilitates community heterogeneity

Although grazers have long been recognized as top-down architects of plant communities, animal roles in determining microbial community composition have seldom been examined, particularly in aboveground systems. To determine the extent to which an animal can shape microbial communities, we conducted a controlled mesocosm study in situ to see if introducing mycophageous tree snails changed phyllosphere fungal community composition relative to matched control mesocosms. Fungal community composition and change was determined by Illumina sequencing of DNA collected from leaf surfaces before snails were introduced, daily for 3 days and weekly for 6 weeks thereafter. Scanning electron microscopy was used to confirm that grazing had occurred, and we recorded 3.5 times more cover of fungal hyphae in control mesocosms compared with those containing snails. Snails do not appear to vector novel microbes and despite grazing, a significant proportion of the initial leaf phyllosphere persisted in the mesocosms. Within-mesocosm diversities of fungi were similar regardless of whether or not snails were added. The greatest differences between the snail-treated and control mesocosms was that grazed mesocosms showed greater infiltration of microbes that were not sampled when the experiment commenced and that the variance in fungal community composition (beta diversity) was greater between leaves in snail-treated mesocosms indicating increased community heterogeneity and ecosystem fragmentation.

Mammalian engineers drive soil microbial communities and ecosystem functions across a disturbance gradient

The effects of mammalian ecosystem engineers on soil microbial communities and ecosystem functions in terrestrial ecosystems are poorly known. Disturbance from livestock has been widely reported to reduce soil function, but disturbance by animals that forage in the soil may partially offset these negative effects of livestock, directly and/or indirectly by shifting the composition and diversity of soil microbial communities. Understanding the role of disturbance from livestock and ecosystem engineers in driving soil microbes and functions is essential for formulating sustainable ecosystem management and conservation policies. We compared soil bacterial community composition and enzyme concentrations within four microsites: foraging pits of two vertebrates, the indigenous short-beaked echidna (Tachyglossus aculeatus) and the exotic European rabbit (Oryctolagus cuniculus), and surface and subsurface soils along a gradient in grazing-induced disturbance in an arid woodland. Microbial community composition varied little across the disturbance gradient, but there were substantial differences among the four microsites. Echidna pits supported a lower relative abundance of Acidobacteria and Cyanobacteria, but a higher relative abundance of Proteobacteria than rabbit pits and surface microsites. Moreover, these microsite differences varied with disturbance. Rabbit pits had a similar profile to the subsoil or the surface soils under moderate and high, but not low disturbance. Overall, echidna foraging pits had the greatest positive effect on function, assessed as mean enzyme concentrations, but rabbits had the least. The positive effects of echidna foraging on function were indirectly driven via microbial community composition. In particular, increasing activity was positively associated with increasing relative abundance of Proteobacteria, but decreasing Acidobacteria. Our study suggests that soil disturbance by animals may offset, to some degree, the oft-reported negative effects of grazing-induced disturbance on soil function. Further, our results suggest that most of this effect will be derived from echidnas, with little positive effects due to rabbits. Activities that enhance the habitat for echidnas or reduce rabbit populations are likely to have a positive effect on soil function in these systems.