Getting to the Root of Tree Soil Microbiome Sampling

Microbiomes play critical roles in host functioning and therefore there is increasing interest in the microbiome assembly of plants. However, sampling strategies for long-lived perennial trees need to be standardised to produce robust data that accurately represents the microbiome over time. This issue is currently unresolved because there is little evidence indicating which portion of perennial tree species (e.g., root region or surrounding soil) is the best to sample to produce the most accurate measure of microbiome communities. Our aim was to sample different compartments of a plant’s belowground microbiome to identify the optimal sampling strategy to account for the microbial community present. We found that the structure of the microbial community depends most strongly on the environment (site) and compartment of sample collected (bulk soil, rhizosphere, or rhizoplane), rather than the depth or cardinal direction of the sample. We also found that the microbial community increased in diversity with increased distance from the tree within the rhizoplane and rhizosphere. The data presented here provides systematic evidence for a pragmatic and robust sampling regime that was tested and validated across different environments and soil types while controlling for host genotype. This sampling regime will enable effective partitioning of root compartments when studying the microbiome associated with perennial tree species, allowing targeted questions about the microbiome to be explored with greater accuracy

The influence of aggregate size fraction and horizon position on microbial community composition

peer-reviewedThe influence of horizon position and aggregate size on bacterial and fungal community composition was determined. From nine sites, soils were collected from the top three horizon positions (H1, H2 and H3). Physical fractionation separated samples into large macroaggregate (LM, >2000 μm), macroaggregate (MAC, >250 μm), microaggregate (MIC, <250 μm), and silt and clay (SC, 53 μm) fractions. In all samples, the structure of the bacterial and fungal community composition was assessed via restriction fragment length polymorphism (T-RFLP), and for the four aggregate sizes from the top two horizons positions an in-depth analysis of the bacterial community was conducted using next generation sequencing (NGS). Bacterial and fungal communities both differed between aggregate-sizes. Changes in the composition of the bacterial and fungal communities also occurred among horizon positions, with a significant interaction between aggregate size and horizon position evident for the bacterial community. Using NGS, it was shown that aggregate-size had a significant effect on the bacterial community in both horizon positions at both the phyla and family taxonomic levels. MAC and MIC significantly differed in the % relative abundance of bacterial groups, potentially indicating differing predation pressures. These results indicate that both horizon position and aggregate size support distinct microbial communities. Understanding these parameters is critical in our comprehension of the patterns of microbial diversity in soil

Microbiome ethics, guiding principles for microbiome research, use and knowledge management

peer-reviewedThe overarching biological impact of microbiomes on their hosts, and more generally their environment, reflects the co-evolution of a mutualistic symbiosis, generating fitness for both. Knowledge of microbiomes, their systemic role, interactions, and impact grows exponentially. When a research field of importance for planetary health evolves so rapidly, it is essential to consider it from an ethical holistic perspective. However, to date, the topic of microbiome ethics has received relatively little attention considering its importance. Here, ethical analysis of microbiome research, innovation, use, and potential impact is structured around the four cornerstone principles of ethics: Do Good; Don’t Harm; Respect; Act Justly. This simple, but not simplistic approach allows ethical issues to be communicative and operational. The essence of the paper is captured in a set of eleven microbiome ethics recommendations, e.g., proposing gut microbiome status as common global heritage, similar to the internationally agreed status of major food crops

Microbiome interconnectedness throughout environments with major consequences for healthy people and a healthy planet

Microbiomes have highly important roles for ecosystem functioning and carry out key functions that support planetary health, including nutrient cycling, climate regulation, and water filtration. Microbiomes are also intimately associated with complex multicellular organisms such as humans, other animals, plants, and insects and perform crucial roles for the health of their hosts. Although we are starting to understand that microbiomes in different systems are interconnected, there is still a poor understanding of microbiome transfer and connectivity. In this review we show how microbiomes are connected within and transferred between different habitats and discuss the functional consequences of these connections. Microbiome transfer occurs between and within abiotic (e.g., air, soil, and water) and biotic environments, and can either be mediated through different vectors (e.g., insects or food) or direct interactions. Such transfer processes may also include the transmission of pathogens or antibiotic resistance genes. However, here, we highlight the fact that microbiome transmission can have positive effects on planetary and human health, where transmitted microorganisms potentially providing novel functions may be important for the adaptation of ecosystems.The European Union’s H2020 Research and Innovation Program and a grant of the Spanish Ministry of Science and Innovation.https://journals.asm.org/journal/mmbram2024Plant Production and Soil ScienceSDG-15:Life on lan

Firmicutes dominate the bacterial taxa within sugar-cane processing plants

Sugar cane processing sites are characterised by high sugar/hemicellulose levels, available moisture and warm conditions, and are relatively unexplored unique microbial environments. The PhyloChip microarray was used to investigate bacterial diversity and community composition in three Australian sugar cane processing plants. These ecosystems were highly complex and dominated by four main Phyla, Firmicutes (the most dominant), followed by Proteobacteria, Bacteroidetes, and Chloroflexi. Significant variation (p , 0.05) in community structure occurred between samples collected from ‘floor dump sediment’, ‘cooling tower water’, and ‘bagasse leachate’. Many bacterial Classes contributed to these differences, however most were of low numerical abundance. Separation in community composition was also linked to Classes of Firmicutes, particularly Bacillales, Lactobacillales and Clostridiales, whose dominance is likely to be linked to their physiology as ‘lactic acid bacteria’, capable of fermenting the sugars present. This process may help displace other bacterial taxa, providing a competitive advantage for Firmicutes bacteria

Shifts in prokaryotic communities under forest and grassland within a tropical mosaic landscape

The Anthropocene is linked to massive land use changes as a result of human activity. While aboveground changes in biodiversity are well documented, the effects on belowground microbial communities are less understood, yet could impact on many ecosystem functions. Here we aimed to identify differences in belowground microbial diversity between forest and grassland sites in a humid tropical mosaic landscape in Papua New Guinea. Using DNA-based amplicon sequencing targeting the 16S rRNA gene, prokaryotic community composition was assessed from surface soil samples. The composition of prokaryotic communities (beta diversity)differed between forest and grassland sites despite maintaining similar richness (alpha diversity) levels. Changes in community structure were small at higher taxonomic levels, but strong at the operational taxonomic unit(OTU) level but for a small subset of taxa. Changes in community composition between sites (based on Bray-Curtis distance) reflected a large rearrangement with species assemblage (OTU) differing by 68%. The results suggest that ecosystem change in this landscape leads to ecological filtering and selection at lower, but not higher taxonomic levels

Characterising the diversity of oomycetes in a multi-use landscape in Aotearoa New Zealand

Te Kaha, rohe of Te Whānau-ā-Apanu, is a multi-use landscape that in recent years has invested in kiwifruit orchard expansion. This transition to a more horticulturally intensive crop will create a greater need for irrigation, and current schemes propose diverting water from the nearby Kereu River. Landowners and kaitiakitanga are cognisant that untreated irrigation water from natural bodies can lead to the dissemination of water-borne plant pathogen propagules, and thus, this research sought to characterise the diversity of oomycetes present in both aquatic and terrestrial sites in the Te Kaha catchment, with a focus on Phytophthora. In January 2023, water samples were collected and filtered at nine positions along a 9.3 km stretch of the Kereu River. Soil samples were also collected from nine sites that featured varying land usage — kiwifruit, maize, and ngahere | native forest. Oomycete specific ITS1 amplicons were generated from water and soil eDNA and sequenced using Illumina MiSeq. Kereu River sites were also baited in situ using a selection of native, exotic, and agriculturally relevant plant leaves. Exotic plant baits were more successful in yielding cultures with morphologies congruent with Phytophthora, whereas native plant baits had a higher incidence of producing isolates with sporangial exit tubes, a feature associated with Pythium. The exact identities of these Phytophthora isolates are being confirmed with Sanger sequencing. Similarity in Oomycota communities between river and soil samples was compared using ANOSIM analysis. Oomycete communities from water were almost entirely distinct from those present in soil (stress = 0.065, R = 0.99, p=0.001). The differences in Oomycota diversity in soils between land usage was also compared, which found significant differences with some overlap in taxa present (stress = 0.074, R = 0.42, p = 0.03). Of the 804 ASV produced, approximately 2% belonged to the Phytophthora genus. Only a third of terrestrial sites had Phytophthora present, whereas Phytophthora were detected in all locations along the Kereu River. Phytophthora spp. belonging to clades 2b and 12 were unique to soils, whereas species belonging to clades 6, 7, and 8 were exclusive to the Kereu River. Only one ASV, belonging to the Clade 2c ‘P. citricola complex’, was found in both terrestrial and aquatic landscapes. While there is currently no evidence of Phytophthora ‘spill-over’ between terrestrial and aquatic systems in Te Kaha, our results suggest that continued monitoring of this catchment could prove beneficial as these neighbouring landscapes increasingly interact in the future

The influence of aggregate size fraction and horizon position on microbial community composition

The influence of horizon position and aggregate size on bacterial and fungal community composition was determined. From nine sites, soils were collected from the top three horizon positions (H1, H2 and H3). Physical fractionation separated samples into large macroaggregate (LM, >2000 μm), macroaggregate (MAC, >250 μm), microaggregate (MIC, <250 μm), and silt and clay (SC, 53 μm) fractions. In all samples, the structure of the bacterial and fungal community composition was assessed via restriction fragment length polymorphism (T-RFLP), and for the four aggregate sizes from the top two horizons positions an in-depth analysis of the bacterial community was conducted using next generation sequencing (NGS). Bacterial and fungal communities both differed between aggregate-sizes. Changes in the composition of the bacterial and fungal communities also occurred among horizon positions, with a significant interaction between aggregate size and horizon position evident for the bacterial community. Using NGS, it was shown that aggregate-size had a significant effect on the bacterial community in both horizon positions at both the phyla and family taxonomic levels. MAC and MIC significantly differed in the % relative abundance of bacterial groups, potentially indicating differing predation pressures. These results indicate that both horizon position and aggregate size support distinct microbial communities. Understanding these parameters is critical in our comprehension of the patterns of microbial diversity in soil