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The significance of biodiversity to biogeochemical cycling is viewed most directly through the specific biogeochemical transformations that organisms perform. Although functional diversity in soils can be great, it is exceeded to a high degree by the richness of soil species. It is generally inferred from this richness that soil systems have a high...
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Context 1
... and vice versa. Throughout much of this work, we relied on measurements of microbial biomass carbon, nitrogen, and phosphorus, to determine the extent of nutrient availability enhanced by faunal feeding on the microbes. Although this provided some information, it avoided the overall question, what microbes are present in the soil and on earth (Fig. 5, Fig. 1. An early soil fungal foodweb, delineated using 65 Zn-labelled soil fungi (Geotrichum sp.). Predatory mite activity arose later in the experiment, in accord with expectations (Coleman and McGinnis, 1970). Whitman et al., 1998)? Which microbes are culturable or not (many are not yet culturable, Fig. 6) and which ones are ...
Context 2
... evidence from field and microcosm studies generally supports the concept that increasing species richness increases stability of ecosystem properties, if one can sort through other confounding variables. Thus, coefficient of variation of aboveground biomass decreased with increasing species richness (Fig. 15A, Hooper et al., 2005). In a microcosm study, the standard deviation of CO 2 efflux from a microbial microcosm decreased with increasing species richness (Fig. 15B, Hooper et al., ...
Context 3
... stability of ecosystem properties, if one can sort through other confounding variables. Thus, coefficient of variation of aboveground biomass decreased with increasing species richness (Fig. 15A, Hooper et al., 2005). In a microcosm study, the standard deviation of CO 2 efflux from a microbial microcosm decreased with increasing species richness (Fig. 15B, Hooper et al., ...
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Citations
... cellulose, lignin), longer generation time of fungal biomass and therefore slower turnover of C. Energy fluxes through bacterial and fungal channels also affect the higher trophic levels of bacterial and fungal grazers. While the major bacterial grazers are protozoa and nematodes [15,16], grazers of fungi are typically fungus-feeding microarthropods [19,20]. In addition to the traditionally known predators of bacteria, several bacterial groups can prey on bacteria as well [15]. ...
Large amounts of terrestrial organic carbon (OC) are stored in Arctic permafrost-affected soils. Through processes of cryoturbation and solifluction, the subsoils can contain subducted topsoil material, which largely contribute to the large OC storage in these soils. While the bacterial, archaeal, and fungal communities in such soils have been studied to some degree, information about protists and meso-and macrofauna is scarce, although these groups might substantially contribute to OC processing, through e.g., food web interactions. Different organic and mineral horizons, including subducted topsoil material, of Arctic soils were investigated using a metatran-scriptomics three-domain community profiling approach. Soil horizons were compared in regards to their total microbial community composition including all three domains of life. Furthermore, abundances of different pro-and eukaryotic micropredators were examined and a variety of functional groups involved in the carbon (C) and the nitrogen (N) cycle were analyzed in relation to specific taxonomic groups and abiotic soil parameters. Our study showed that RNA yields positively correlated with the OC content of the horizon and that the composition of the microbial community in subducted topsoil material rather matched that of mineral subsoils instead of organic top horizons. Horizon-resolved profiling revealed heterogeneity in the associated microbiomes and showed major differences in microbiomes of topsoil and subducted topsoil. The abundance of protist and nematode micropredators decreased in subducted topsoil, while predatory myxobacteria remained remarkably constant and comprised high proportions of the total communities in all horizons. Correlations analysis between functional guilds and biotic and abiotic parameters suggest a major impact of predatory myxobacteria on carbon and nitrogen cycles of subducted topsoils. The study adds urgently needed information about the total biota structure in permafrost soils and first insights into the associated soil microbial food webs.
... Long-term cultivation of several crops in a crop system can supply the soil with a diversity of organic compounds due to the composition of the plant tissue, root system and exudates (Haichar et al., 2014;Turner et al., 2013). Thus, the richness of crop species may positively influence the metabolic activity and modulate the microbial community (Beare et al., 1995;Grayston et al., 2001;Liang et al., 2017) and, as a consequence, SOM composition. ...
... Given that rates are already slow, the plastisphere microbial community tends to be less crucial for influencing plastic mobility in soil, and movement is not as important for sampling the source microbial community. The second major difference is that soils are extremely heterogeneous 39 and particle rich 48 , with plastic debris also being incorporated into the main building blocks of soil structure, the soil aggregates 49 . As a consequence, different plastic particles in a given soil will be exposed Fig. 1 | The definition of the soil plastisphere and its place in the context of other soil compartments. ...
... The microbial community of the plastisphere consists not only of the attached biofilm (or microorganisms colonizing the plastic surface) but also of the microorganisms in the soil under the influence of the plastic particle. b, The soil plastisphere in the context of other important soil features and hotspots 39,48 , such as the rhizosphere (soil under the influence of roots 50 ), the aggregatusphere (soil aggregates as major building blocks of soil structure 101 ), the drilosphere (soil influenced by earthworms 102 ) and the detritusphere (soil under the influence of dead organic material (detritus) 103 ). The soil plastisphere also encompasses the soil under the direct influence of plastic particles, which includes not only the biotic community but also the changed physico-chemical soil environment itself (the plastic surface is depicted as the grey structure in the centre of the figure, surrounded by the yellow shading, symbolizing the soil under the immediate influence of plastic). ...
... In soil, microorganisms are spatially ('hotspots'; small soil volumes with much faster and more intensive microbial processes) and temporally ('hot moments'; short-term events with accelerated microbial processes) activated by the input of available carbon sources or other environmental factors such as soil moisture content 48 . Areas in soil that are hotspots of microbial activity include the rhizosphere, the drilosphere (soil under the influence of earthworms), the detritusphere (litter layer) and soil aggregates 39 . These soil compartments are characterized by higher microbial abundance, diversity and activity 48 compared with the bulk soil. ...
Understanding the effects of plastic pollution in terrestrial ecosystems is a priority in environmental research. A central aspect of this suite of pollutants is that it entails particles, in addition to chemical compounds, and this makes plastic quite different from the vast majority of chemical environmental pollutants. Particles can be habitats for microbial communities, and plastics can be a source of chemical compounds that are released into the surrounding environment. In the aquatic literature, the term 'plastisphere' has been coined to refer to the microbial community colonizing plastic debris; here, we use a definition that also includes the immediate soil environment of these particles to align the definition with other concepts in soil microbiology. First, we highlight major differences in the plastisphere between aquatic and soil ecosystems, then we review what is currently known about the soil plastisphere, including the members of the microbial community that are enriched, and the possible mechanisms underpinning this selection. Then, we focus on outlining future prospects for research on the soil plastisphere.
... Root exudates can increase arsenic mobilization and their production increases over the growing season (Aulakh et al. 2001;Tu et al. 2004). In fact, the larger microbial biomass throughout the growing season is, in part, related to the increasing availability of plant-derived carbon (Beare et al. 1995;Lu et al. 2002;Vezzani et al. 2018). There was greater root mass in the RH treatment at maturity relative to the CH and VH treatments (Fig. 6a), implying a greater ability to exude carbon to feed the microbial community (Beare et al. 1995). ...
... In fact, the larger microbial biomass throughout the growing season is, in part, related to the increasing availability of plant-derived carbon (Beare et al. 1995;Lu et al. 2002;Vezzani et al. 2018). There was greater root mass in the RH treatment at maturity relative to the CH and VH treatments (Fig. 6a), implying a greater ability to exude carbon to feed the microbial community (Beare et al. 1995). This observation supports the idea that the stronger response to temperature during ripening could be linked to root-exuded carbon in combination with a larger, more active microbial community. ...
Purpose
Arsenic is a frequent contaminant of rice. Recent studies show that elevated temperatures, like those from climate change, can further increase arsenic concentrations in rice. It is still unclear if the timing of heat exposure relative to plant development influences the magnitude and allocation of arsenic accumulation in rice plants.
Method
We grew potted rice plants from seedlings until maturity in growth chambers with different temperature regimes: baseline (26 °C/22 °C, day/night), continuously elevated (30 °C/27 °C), baseline with a 20-day heat spike during the vegetative stage, and baseline with a 20-day heat spike during the ripening stage. Heat spikes mimicked the elevated temperature.
Results
Concentrations of arsenic in both porewater and plant tissues were uniformly higher in the continuously elevated treatment relative to the baseline treatment. A heat spike during the ripening stage caused a marked increase in arsenic mobilization into porewater. A heat spike in the vegetative stage caused a short-term increase in arsenic concentrations in plant tissue but this relative increase did not persist to maturity. Plants that experienced a heat spike in the ripening stage had an increase in arsenic concentrations within various tissue types at maturity.
Conclusion
Differential responses to the two heat spikes may be due to less soil microbial and plant biomass during the vegetative stage, as well as reduced root biomass caused by heat stress during the vegetative stage. Our results demonstrate that both continuous and short-term increases in temperature later in plant development can heighten dietary arsenic exposure to rice consumers.
... Se ha intentado conceptualizar la dinámica de la vida en el suelo, a través de las llamadas esferas de influencia biológicamente relevantes (Beare et al.,1995) o también conocidas como dominios funcionales (Lavelle, 2000). Estas esferas son las que regulan las interacciones entre los organismos en el suelo y han sido definidas como: detritósfera (masa de restos vegetales y animales en la capa superficial del suelo), rizósfera (esfera de influencia alrededor de las raíces, donde se genera una atmósfera compleja y dinámica a partir de los exudados de estas), drilósfera (volumen de suelo bajo la influencia de lombrices de tierra), agregatósfera (agrupación jerárquica y unidades organizadas de componentes y minerales, micro y macro orgánicos), porósfera (disposición de los espacios disponibles para la vida, de tamaños variables, derivados de la actividad de raíces y macro fauna) (Beare et al., 1995;Brown et al., 2000;Coleman, 2008). ...
... Se ha intentado conceptualizar la dinámica de la vida en el suelo, a través de las llamadas esferas de influencia biológicamente relevantes (Beare et al.,1995) o también conocidas como dominios funcionales (Lavelle, 2000). Estas esferas son las que regulan las interacciones entre los organismos en el suelo y han sido definidas como: detritósfera (masa de restos vegetales y animales en la capa superficial del suelo), rizósfera (esfera de influencia alrededor de las raíces, donde se genera una atmósfera compleja y dinámica a partir de los exudados de estas), drilósfera (volumen de suelo bajo la influencia de lombrices de tierra), agregatósfera (agrupación jerárquica y unidades organizadas de componentes y minerales, micro y macro orgánicos), porósfera (disposición de los espacios disponibles para la vida, de tamaños variables, derivados de la actividad de raíces y macro fauna) (Beare et al., 1995;Brown et al., 2000;Coleman, 2008). ...
... The rhizosphere is described as the most active interface on Earth since it is home to numerous living microorganisms and invertebrates [5]. Soil microbes are involved in many critical ecosystem processes, such as nutrient acquisition, biogeochemical cycling [6], and soil aggregation [7], and they play a significant role in the development of sustainable agriculture [8][9][10]. In addition, soil microbes strongly influence plant productivity through direct or indirect effects [8]. ...
Two different qualities of pumpkin, cultivars G1519 and G1511, were grown in the same environment under identical management. However, their qualities, such as the contents of total soluble solids, starch, protein, and vitamin C, were significantly different. Do rhizospheric microbes contribute to pumpkin quality? To answer this question, this study investigated the soil microbial compositions in the rhizospheres of different quality pumpkin cultivars to determine the differences in these soil microbial compositions and thus determine how soil microbes may affect pumpkin quality. Firstly, a randomized complete block design with two pumpkin cultivars and three replications was performed in this study. The soil microbial compositions and structures in the rhizospheres of the two pumpkin cultivars were analyzed using a high-throughput sequencing technique. In comparison with the low-quality pumpkin cultivar (G1519), higher microbial diversity and richness could be found in the rhizospheres of the high-quality pumpkin cultivar (G1511). The results showed that there were significant differences in the soil bacterial and fungal community compositions in the rhizospheres of the high- and low-quality pumpkin cultivars. Although the compositions and proportions of microorganisms were similar in the rhizospheres of the two pumpkin cultivars, the proportions of Basidiomycota and Micropsalliota in the G1519 rhizosphere were much higher than those in the G1511 rhizosphere. Furthermore, the fungal phylum and genus Rozellomycota and Unclassified_p__Rozellomycota were unique in the rhizosphere of the high-quality pumpkin cultivar (G1511). All the above results indicate that soil microbes were enriched differentially in the rhizospheres of the low- and high-quality pumpkin cultivars. In other words, more abundant soil microbes were recruited in the rhizosphere of the high-quality pumpkin cultivar as compared to that of the low-quality cultivar. Rozellomycota and Unclassified_p__Rozellomycota may be functional microorganisms relating to pumpkin quality.
... De acordo com Beare et al. (1995), a drilosfera (do gr, drilus: minhoca) corresponde à zona do solo diretamente influenciada pela ação das minhocas, onde se pode observar a presença de galerias (potencia o crescimento das raízes das plantas), coprólitos que podem ser utilizados por outros organismos para a sua alimentação (os coprólitos são hotspots de microrganismos), muco e carga microbiana (Lavelle et al., 1989). Devido à sua atividade no solo, as minhocas foram consideradas engenheiros do ecossistema por Jones et al. (1994). ...
Diariamente são libertadas substâncias tóxicas no ambiente que entram nos ecossistemas aquáticos e terrestres tais como metais, pesticidas, plásticos, fármacos, entre outros, provocando efeitos nefastos nos organismos expostos. Por outro lado, a contaminação dos solos agrícolas contribui para a contaminação das cadeias alimentares afetando os organismos terrestres e mais tarde o Homem.
... Microbial communities on plastic surfaces typically differ from the adjacent soil microbiome and exhibit reduced diversity compared to soil (Bandopadhyay et al. 2018(Bandopadhyay et al. , 2020Huang et al. 2019;Rüthi et al. 2020;Yi et al. 2021;Zhang et al. 2019a;Zhou et al. 2021). Thus, analogous to other biologically relevant spheres in soil, such as the rhizosphere (Beare et al. 1995), the plastisphere in soil forms a new type of microbial habitat encompassing MP surfaces and the adjacent soil influenced by MP (Rüthi et al. 2020;Zhou et al. 2021). Changes in microbial composition and abundance may be due to the use of MP as a substrate by specific microorganisms ). ...
Microplastics (MP, plastic particles between 0.1 and 5000 μm) contaminate agricultural soils through the application of organic fertilizers, sewage sludge, and plastic mulch. MP surfaces and the MP-soil interface provide specific habitats for soil microorganisms—the plastisphere. Microorganisms in the plastisphere may benefit from utilizing MP as a carbon (C) source. Hydrolyzable MP with ester bonds are susceptible to enzymatic depolymerization by hydrolysis. In a microcosm experiment, we investigated MP biodegradation of small and large (< 0.5 mm and 0.5–2 mm respectively), hydrolyzable (a poly(lactic acid)/poly(butylene co-adipate terephthalate) blend, PLA/PBAT) and non-hydrolyzable (low-density polyethylene, LDPE) polymers, and the effects of these MP on microorganisms in dry and wet MP-amended soil. MP affected neither abundance and composition of the main soil microbial groups (fungi, Gram-negative, and Gram-positive bacteria), specific activities of ß-glucosidase, ß-xylosidase, lipase, and phenoloxidase, nor respiration in MP-amended soil. Only large PLA/PBAT particles in dry soil were significantly mineralized (15.4% of initial PLA/PBAT-C after 230 days). PLA/PBAT mineralization coincided with enhanced lipase and ß-glucosidase activities on the surfaces of individual PLA/PBAT particles extracted from the soil after incubation (compared to LDPE and non-incubated PLA/PBAT particles). We detected cracks on the surfaces of PLA/PBAT particles using scanning electron microscopy, indicating initiation of MP biodegradation, presumably due to depolymerization by lipases. Results suggest that the PLA/PBAT plastisphere is a polymer-specific habitat for lipase-producing soil microorganisms. Our study demonstrates that analyzing biogeochemical interactions within polymer-specific plastispheres is essential to assess MP fate and their impacts on microbially driven soil processes.
... Macroinvertebrates can be characterized on a size-class basis, as size-class delineation does not take away from the essential role of invertebrates involved in brown food webs, resource redistribution, and decomposition. Soil macroinvertebrates, ranging from earthworms, soil-dwelling insects, myriapods, isopods, and Staphylinids, are of a size class larger than 2 mm [56,57] and differ from the meso fauna that are between 0.1 mm and 0.2 mm [13,58,59]. The manipulation of invertebrate presence, absence, or density can require laborious sterilization or inoculation in a controlled setting [60], but as it relates to this study, polyester mesh (0.22 mm) was used to restrict macroinvertebrates from interacting with decomposing wood substrate placed in the root zone of 6 AM and 7 EM trees. ...
Woodlands are pivotal to carbon stocks, but the process of cycling C is slow and may be most effective in the biodiverse root zone. How the root zone impacts plants has been widely examined over the past few decades, but the role of the root zone in decomposition is understudied. Here, we examined how mycorrhizal association and macroinvertebrate activity influences wood decomposition across diverse tree species. Within the root zone of six predominantly arbuscular mycor-rhizal (AM) (Acer negundo, Acer saccharum, Prunus serotina, Juglans nigra, Sassafras albidum, and Liri-odendron tulipfera) and seven predominantly ectomycorrhizal (EM) tree species (Carya glabra, Quer-cus alba, Quercus rubra, Betula alleghaniensis, Picea rubens, Pinus virginiana, and Pinus strobus), woody litter was buried for 13 months. Macroinvertebrate access to woody substrate was either prevented or not using 0.22 mm mesh in a common garden site in central Pennsylvania. Decomposition was assessed as proportionate mass loss, as explained by root diameter, phylogenetic signal, mycorrhi-zal type, canopy tree trait, or macroinvertebrate exclusion. Macroinvertebrate exclusion significantly increased wood decomposition by 5.9%, while mycorrhizal type did not affect wood decomposition , nor did canopy traits (i.e., broad leaves versus pine needles). Interestingly, there was a phylogenetic signal for wood decomposition. Local indicators for phylogenetic associations (LIPA) determined high values of sensitivity value in Pinus and Picea genera, while Carya, Juglans, Betula, and Prunus yielded low values of sensitivity. Phylogenetic signals went undetected for tree root morphology. Despite this, roots greater than 0.35 mm significantly increased woody litter decomposition by 8%. In conclusion, the findings of this study suggest trees with larger root diameters can accelerate C cycling, as can trees associated with certain phylogenetic clades. In addition, root zone macroinvertebrates can potentially limit woody C cycling, while mycorrhizal type does not play a significant role.
... They account for up to 90% of total soil microbiota and microfauna biomass (Metting, 1993). Soil microbial communities are involved in respiration, decomposition, nutrient absorption and fixation, heavy metal detoxification bioremediation, and serve as global carbon sinks (Schlesinger, 1991;Beare et al., 1995;Chua et al., 2021). There are around 10 billion microorganisms that could be found in one gram of soil, and it possibly constituted of many unique species (Roselló-Mora and Amann, 2001). ...
Elucidation of the three-dimensional (3D) structure of biological macromolecules (e.g.
proteins, nucleic acids, protein-protein complexes or protein-nucleic acid complexes) is the
main key in the niche of structural biology to infer how the proteins function in cells (Hauri et
al., 2019). The availability of atomic resolution structures, researchers are able to understand
the protein function and help to unveil the protein mechanisms and the inner workings of the
living cell. A better understanding of molecular structure and function also contributes to
strategies for drug development, with deliberate design in medicinal chemistry, agrochemical
and pharmaceutical products. Currently, more than 80% of the Protein Data Bank (rcsb-PDB)
deposited entries are protein structures that were determined using X-ray crystallography. The
most vital step to obtain crystals for crystallographic studies is to purify target protein to
homogeneity or as close to 100% purity. The purity of the purified protein is the key factor in
obtaining high-resolution crystal diffractions (Hashizume et al., 2020). Protein crystals are
obtained when the target macromolecules are brought to supersaturation. Therefore, normally
the protein sample will be concentrated to the highest possible concentration in the range of 1
mg/mL to 50 mg/mL without causing protein precipitation or /and aggregation. Precipitating
agents are used in crystallization to generate solid (crystals) from the solution. When a protein
is exposed to a precipitating agent, this will normally promote the nucleation of crystals in the
solution depending on the protein purity, three-dimensional crystals will grow from the solution
(Chernov, 2003; Niedzialkowska et al., 2016). The formation of crystals is initiated by
supersaturation which is achieved when the concentration of the solute is higher than its
solubility. This chapter focuses on one of the techniques to obtain protein crystals which is the
vapor diffusion technique. A setup for vapor diffusion which is called the hanging drop and itting drop methods is demonstrated. In addition, the optimization methods to get better quality
crystals are explained in this section. Crystal optimization is normally done if the initial
crystallization conditions (crystal hits) is insufficient for diffraction either when the crystal size
is too small, or the diffraction result is very poor for structural elucidation. Unfortunately, in a
real case scenario, the first round of initial hit is normally insufficient for diffraction. Five
methods of crystal optimization are described which are 1) screening using a grid, 2)
microseeding, 3) additives, 4) cryoprotectants and 5) crystal dehydration. For each of the
methods, an example of protein crystals is provided that were obtained from our study,
Antarctic yeast T-Complex Protein (TCP-1).
