A buried Neolithic paddy soil reveals loss of microbial functional diversity after modern rice cultivation

Phosphate-Solubilizing Bacteria: Advances in Their Physiology, Molecular Mechanisms and Microbial Community Effects

Phosphorus is an essential nutrient for all life on earth and has a major impact on plant growth and crop yield. The forms of phosphorus that can be directly absorbed and utilized by plants are mainly HPO42- and H2PO4-, which are known as usable phosphorus. At present, the total phosphorus content of soils worldwide is 400-1000 mg/kg, of which only 1.00-2.50% is plant-available, which seriously affects the growth of plants and the development of agriculture, resulting in a high level of total phosphorus in soils and a scarcity of available phosphorus. Traditional methods of applying phosphorus fertilizer cannot address phosphorus deficiency problems; they harm the environment and the ore material is a nonrenewable natural resource. Therefore, it is imperative to find alternative environmentally compatible and economically viable strategies to address phosphorus scarcity. Phosphorus-solubilizing bacteria (PSB) can convert insoluble phosphorus in the soil into usable phosphorus that can be directly absorbed by plants, thus improving the uptake and utilization of phosphorus by plants. However, there is no clear and systematic report on the mechanism of action of PSB. Therefore, this paper summarizes the discovery process, species, and distribution of PSB, focusing on the physiological mechanisms outlining the processes of acidolysis, enzymolysis, chelation and complexation reactions of PSB. The related genes regulating PSB acidolysis and enzymatic action as well as genes related to phosphate transport and the molecular direction mechanism of its pathway are examined. The effects of PSB on the structure and abundance of microbial communities in soil are also described, illustrating the mechanism of how PSB interact with microorganisms in soil and indirectly increase the amount of available phosphorus in soil. And three perspectives are considered in further exploring the PSB mechanism in utilizing a synergistic multi-omics approach, exploring PSB-related regulatory genes in different phosphorus levels and investigating the application of PSB as a microbial fungicide. This paper aims to provide theoretical support for improving the utilization of soil insoluble phosphorus and providing optimal management of elemental phosphorus in the future.

Inter-bacterial mutualism promoted by public goods in a system characterized by deterministic temperature variation

Mutualism is commonly observed in nature but not often reported for bacterial communities. Although abiotic stress is thought to promote microbial mutualism, there is a paucity of research in this area. Here, we monitor microbial communities in a quasi-natural composting system, where temperature variation (20 °C-70 °C) is the main abiotic stress. Genomic analyses and culturing experiments provide evidence that temperature selects for slow-growing and stress-tolerant strains (i.e., Thermobifida fusca and Saccharomonospora viridis), and mutualistic interactions emerge between them and the remaining strains through the sharing of cobalamin. Comparison of 3000 bacterial pairings reveals that mutualism is common (~39.1%) and competition is rare (~13.9%) in pairs involving T. fusca and S. viridis. Overall, our work provides insights into how high temperature can favour mutualism and reduce competition at both the community and species levels.

Changes in the Microbial Structure of the Root Soil and the Yield of Chinese Baby Cabbage by Chemical Fertilizer Reduction with Bio-Organic Fertilizer Application

Using high-throughput sequencing, this study aimed to explore the response of soil microbial community and Chinese baby cabbage yield to the reduction of chemical fertilizers combined with bio-organic fertilizer. Our experiments consisted of conventional fertilizer (CK), 30% chemical fertilizer reduction + 6,000 kg/ha bio-organic fertilizer (T1), 30% chemical fertilizer reduction + 9,000 kg/ha bio-organic fertilizer (T2), 40% chemical fertilizer reduction + 6,000 kg/ha bio-organic fertilizer (T3), and 40% chemical fertilizer reduction + 9,000 kg/ha bio-organic fertilizer (T4). Compared with CK, soil microbial diversity and richness were higher for all treatments with added bio-organic fertilizer. Principle coordinate analysis (PCoA) showed that the bacterial and fungal communities in T2 and T4 were similar to each other. Redundancy and Spearman's correlation analyses of microbial communities and soil physicochemical properties revealed that reductions in chemical fertilizer rate combined with bio-organic fertilizer had a stronger impact on the fungal than the bacterial community. They also increased the relative abundance of the dominant bacterial and fungal phyla. Chinese baby cabbage yield was relatively higher under the combined bio-organic fertilizer plus reduced chemical fertilizer rate with T2 showing the highest yield. Therefore, this approach is feasible for sustainable agricultural, cost-effective and profitable crop production. IMPORTANCE Chemical fertilizers are commonly used for agriculture, though bio-organic fertilizers may be more efficient. We found that a mixture of bio-organic and moderately reduced chemical fertilizer was more effective than chemical fertilizer alone, as it raised the Chinese baby cabbage yield. Further, the presence of bio-organic fertilizer enhanced overall soil physicochemistry, as well as improved the beneficial bacterial and fungal abundance and diversity. Thus, we found that fertilizer combination sustainably & cost-effectively improves crop & soil quality.

Environmental stress-discriminatory taxa are associated with high C and N cycling functional potentials in dryland grasslands

Increasing environmental stress strongly affects soil microbial communities, but the responses of the microbial assembly and the functional potential of the dominant microbial community in the presence of environmental stress in drylands are still poorly understood. Here, we undertook a broad appraisal of the abundance, diversity, similarity, community assembly, network properties and functions of soil microbiomes in 82 dryland grasslands along environmental gradients. We found that the bacterial and fungal diversity and community similarity showed different sensitivities to environmental stress (decreased mean annual precipitation (MAP) and soil nutrient levels and increased soil pH), and MAP was the most important factor influencing microbial community patterns. In addition, the dominant subcommunity of both bacteria and fungi was more sensitive to environmental stress than the nondominant subcommunity. Although increasing environmental stress decreased microbial phylogenetic clustering, it had no effects on the stochastic and deterministic assembly process balance. Moreover, we identified 101 bacterial and 34 fungal environmental stress-discriminatory taxa that were sensitive to environmental stress, and these bacterial markers showed a high correlation with the abundance of carbon (C) and nitrogen (N) cycling-related genes, whereas the taxa classified as connectors in the network were mainly correlated with C degradation genes. Our study shows that the different responses of bacteria and fungi to environmental stress bring challenges to predicting microbial function, but a relatively small number of taxa play an important role in driving C and N cycling-related functional genes, indicating that identifying an organism's phenotypic characteristics or traits of key taxa may improve our knowledge of the microbial response to ongoing global changes.

Benefits of phosphate solubilizing bacteria on belowground crop performance for improved crop acquisition of phosphorus

Although research on plant growth promoting bacteria began in the 1950s, basic and applied research on bacteria improving use of phosphorus (P) continues to be a priority among many agricultural research institutions. Ultimately, identifying agriculturally beneficial microbes, notably P solubilizing bacteria (PSB), that enhance the efficient use of P supports more sustainable cropping systems and the judicious use of mineral nutrients. In parallel, there is more attention on improving crop root P acquisition of existing soil P pools as well as by increasing the proportion of fertilizer P that is taken up by crops. Today, new lines of research are emerging to investigate the co-optimization of PSB-fertilizer-crop root processes for improved P efficiency and agricultural performance. In this review, we compile and summarize available findings on the beneficial effects of PSB on crop production with a focus on crop P acquisition via root system responses at the structural, functional and transcriptional levels. We discuss the current state of knowledge on the mechanisms of PSB-mediated P availability, both soil- and root-associated, as well as crop uptake via P solubilization, mineralization and mobilization, mainly through the production of organic acids and P-hydrolyzing enzymes, and effects on phytohormone signaling for crop root developement. The systematic changes caused by PSB on crop roots are discussed and contextualized within promising functional trait-based frameworks. We also detail agronomic profitability of P (mineral and organic) and PSB co-application, in amended soils and inoculated crops, establishing the connection between the influence of PSB on agroecosystem production and the impact of P fertilization on microbial diversity and crop functional traits for P acquisition.

Metagenomic Insight into the Community Structure of Maize-Rhizosphere Bacteria as Predicted by Different Environmental Factors and Their Functioning within Plant Proximity

The rhizosphere microbiota contributes immensely to nutrient sequestration, productivity and plant growth. Several studies have suggested that environmental factors and high nutrient composition of plant's rhizosphere influence the structural diversity of proximal microorganisms. To verify this assertion, we compare the functional diversity of bacteria in maize rhizosphere and bulk soils using shotgun metagenomics and assess the influence of measured environmental variables on bacterial diversity. Our study showed that the bacterial community associated with each sampling site was distinct, with high community members shared among the samples. The bacterial community was dominated by Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, Bacteroidetes and Verrucomicrobia. In comparison, genera such as Gemmatimonas, Streptomyces, Conexibacter, Burkholderia, Bacillus, Gemmata, Mesorhizobium, Pseudomonas and Micromonospora were significantly (p ≤ 0.05) high in the rhizosphere soils compared to bulk soils. Diversity indices showed that the bacterial composition was significantly different across the sites. The forward selection of environmental factors predicted N-NO₃ (p = 0.019) as the most influential factor controlling the variation in the bacterial community structure, while other factors such as pH (p = 1.00) and sulfate (p = 0.50) contributed insignificantly to the community structure of bacteria. Functional assessment of the sampling sites, considering important pathways viz. nitrogen metabolism, phosphorus metabolism, stress responses, and iron acquisition and metabolism could be represented as Ls > Rs > Rc > Lc. This revealed that functional hits are higher in the rhizosphere soil than their controls. Taken together, inference from this study shows that the sampling sites are hotspots for biotechnologically important microorganisms.

Metagenomics Assessment of Soil Fertilization on the Chemotaxis and Disease Suppressive Genes Abundance in the Maize Rhizosphere

Soil fertility is a function of the level of organic and inorganic substances present in the soil, and it influences the activities of soil-borne microbes, plant growth performance and a host of other beneficial ecological functions. In this metagenomics study, we evaluated the response of maize microbial functional gene diversity involved in chemotaxis, antibiotics, siderophores, and antifungals producing genes within the rhizosphere of maize plants under compost, inorganic fertilizer, and unfertilized conditions. The results show that fertilization treatments at higher compost manure and lower inorganic fertilizer doses as well as maize plants itself in the unfertilized soil through rhizosphere effects share similar influences on the abundance of chemotaxis, siderophores, antifungal, and antibiotics synthesizing genes present in the samples, while higher doses of inorganic fertilizer and lower compost manure treatments significantly repress these genes. The implication is for a disease suppressive soil to be achieved, soil fertilization with high doses of compost manure fertilizer treatments as well as lower inorganic fertilizer should be used to enrich soil fertility and boost the abundance of chemotaxis and disease suppressive genes. Maize crops also should be planted sole or intercropped with other crops to enhance the rhizosphere effect of these plants in promoting the expression and abundance of these beneficial genes in the soil.

Response of the microbial community to phosphate-solubilizing bacterial inoculants on Ulmus chenmoui Cheng in Eastern China

Phosphate-solubilizing bacteria (PSB) have beneficial effects on plant health and soil composition. To date, studies of PSB in soil have largely been performed under field or greenhouse conditions. However, less is known about the impact of introducing indigenous PSB in the field, including their effects on the local microbial community. In this study, we conducted greenhouse and field experiments to explore the effects of the addition of indigenous PSB on the growth of Chenmou elm (Ulmus chenmoui) and on the diversity and composition of the bacterial community in the soil. We obtained four bacterial isolates with the highest phosphate-solubilizing activity: UC_1 (Pseudomonas sp.), UC_M (Klebsiella sp.), UC_J (Burkholderia sp.), and UC_3 (Chryseobacterium sp.). Sequencing on the Illumina MiSeq platform showed that the inoculated PSB did not become the dominant strains in the U. chenmoui rhizosphere. However, the soil bacterial community structure was altered by the addition of these PSB. The relative abundance of Chloroflexi decreased significantly in response to PSB application in all treatment groups, whereas the populations of several bacteria, including Proteobacteria and Bacteroidetes, increased. Network analysis indicated that Chloroflexi was the most strongly negatively correlated with Proteobacteria, whereas Proteobacteria was strongly positively correlated with Bacteroidetes. Our findings indicate that inoculation with PSB (UC_1, UC_M, UC_J, and UC_3) can improve the growth of U. chenmoui and regulate its rhizosphere microbial community. Therefore, inoculation with these bacterial strains could promote the efficient cultivation and production of high-quality plant materials.

Soil fertilization affects the abundance and distribution of carbon and nitrogen cycling genes in the maize rhizosphere

Soil microbes perform important functions in nitrogen and carbon cycling in the biosphere. Microbial communities in the rhizosphere enhance plants' health and promote nutrient turnover and cycling in the soil. In this study, we evaluated the effects of soil fertilization with organic and inorganic fertilizers on the abundances and distribution of carbon and nitrogen cycling genes within the rhizosphere of maize plants. Our result showed that maize plants through rhizosphere effects selected and enriched the same functional genes glnA, gltB, gudB involved in nitrogen cycle as do high compost and low inorganic fertilizer treatments. This observation was significantly different from those of high doses of inorganic fertilizer and low compost manure treated soil. Only alpha amylase encoding genes were selectively enriched by low compost and high inorganic fertilized soil. The other treatments only selected xynB (in Cp8), lacZ (Cp4), bglA, pldB, trpA (N2), uidA (N1) and glgC, vanA (Cn0) carbon cycling genes in the rhizosphere of maize. Also Actinomycetales are selected by high compost, low inorganic fertilizer and control. The control was without any fertilization and the soil was planted with maize. Bacillales are also promoted by low compost and high inorganic fertilizer. This indicated that only microbes capable of tolerating the stress of high dose of inorganic fertilizer will thrive under such condition. Therefore, soil fertilization lowers nitrogen gas emission as seen with the high abundance of nitrogen assimilation genes or microbial anabolic genes, but increases carbon dioxide evolution in the agricultural soil by promoting the abundance of catabolic genes involve in carbon cycling.

Metagenomes of Maize Rhizosphere Samples after Different Fertilization Treatments at Molelwane Farm, Located in North-West Province, South Africa

The need for sustainable agriculture is a global issue that requires urgent attention, particularly in the areas of soil fertility enhancement and management. In this study, the effects of organic and inorganic fertilizers on the rhizosphere microbial communities of maize plants were evaluated.

Abundance of kinless hubs within soil microbial networks are associated with high functional potential in agricultural ecosystems

Microbial taxa within complex ecological networks can be classified by their universal roles based on their level of connectivity with other taxa. Highly connected taxa within an ecological network (kinless hubs) are theoretically expected to support higher levels of ecosystem functions than less connected taxa (peripherals). Empirical evidence of the role of kinless hubs in regulating the functional potential of soil microbial communities, however, is largely unexplored and poorly understood in agricultural ecosystems. Here, we built a correlation network of fungal and bacterial taxa using a large-scale survey consisting of 243 soil samples across functionally and economically important agricultural ecosystems (wheat and maize); and found that the relative abundance of taxa classified as kinless hubs within the ecological network are positively and significantly correlated with the abundance of functional genes including genes for C fixation, C degradation, C methanol, N cycling, P cycling and S cycling. Structural equation modeling of multiple soil properties further indicated that kinless hubs, but not provincial, connector or peripheral taxa, had direct significant and positive relationships with the abundance of multiple functional genes. Our findings provide novel evidence that the relative abundance of soil taxa classified as kinless hubs within microbial networks are associated with high functional potential, with implications for understanding and managing (through manipulating microbial key species) agricultural ecosystems at a large spatial scale.

High starter phosphorus fertilization facilitates soil phosphorus turnover by promoting microbial functional interaction in an arable soil

Microbial phosphorus (P) turnover is critical in C utilization efficiency in agroecosystems. It is therefore necessary to understand the P mobilization processes occurring during P fertilization in order to ensure both crop yield and environmental quality. Here, we established a controlled pot experiment containing soil amended with three different levels of starter P fertilizer and collected soil samples after 30, 60, and 90 days of incubation. Quantitative microbial element cycling (QMEC) smart chip technology and 16S rRNA gene sequencing were used to investigate functional gene structures involved in carbon, nitrogen and P cycling and the bacterial community composition of the collected samples. Although P fertilization did not significantly affect the structure of the soil microbial community, some rare microbiota were changed in particular phosphorus-solubilizing bacteria were enriched at the high P fertilization level, suggesting that the rare taxa make an important contribution to P turnover. P fertilization also altered the functional gene structure, and high P concentrations enhanced the functional gene diversity and abundance. Partial redundancy analysis further revealed that changes in rare taxa and functional genes of soil microorganisms drive the alteration of soil P pools. These findings extend our understanding of the microbial mechanisms of P turnover.

Effects of inorganic and organic treatments on the microbial community of maize rhizosphere by a shotgun metagenomics approach

Purpose

The main drivers of biogeochemical cycling of nutrients, plant growth promotion, and disease suppression are microbes. Organic manure increases soil quality and plant productivity; the same is true of inorganic fertilizer. In this study, we explored shotgun metagenomics study to investigate how maize (Zea mays everta) rhizosphere microbial community diversity is shaped following the application of both compost manure and inorganic fertilizer.

Methods

We used high throughput next-generation sequencing—metagenomics studies to examine the rhizosphere microbial community of maize plants grown in an organic compost manure (8 tons/ha and 4 tons/ha) and inorganic (120 kg/ha NPK and 60 kg/ha NPK chemical) fertilized soils. An unfertilized soil was used as a control.

Results

The taxonomic analysis of the soil revealed that regardless of the fertilization regimes, Proteobacteria and Bacteroidetes are distributed across all the samples, but in varying populations. Higher quantities of organic manure (8 tons/ha) and lower (60 kg/ha) nitrogen fertilizer, as well as the untreated control, supports the selection and enrichment of Proteobacteria and Actinobacteria, while lower quantities of organic compost (4 tons/ha) manure boost the population of Bacteroidetes. Firmicutes, on the other hand, were most abundant in low organic manure (4 tons/ha) and higher inorganic (120 kg/ha) fertilized soil. Fungi were selected and enriched by higher (8 tons/ha) and lower (4 tons/ha) compost manure, while archaea were mostly supported by higher doses of inorganic fertilizers (120 kg/ha) and high compost manure (8 tons/ha) treatments.

Conclusion

Therefore, comprehending the effects of compost and chemical fertilizers (NPK—20% nitrogen, 7% phosphorus, 3% potassium) on the community structure, dynamics, and abundance of rhizosphere microbiome will help in the manipulation of soil microbial community to increase microbial diversity in the agroecosystem.

Niche differentiation of denitrifying anaerobic methane oxidizing bacteria and archaea leads to effective methane filtration in a Tibetan alpine wetland

Denitrifying anaerobic methane oxidation (DAMO) is a vital methane sink in wetlands. However, the interactions and niche partitioning of DAMO bacteria and archaea in freshwater wetland soils, in addition to the interactions among microorganisms that couple methane and nitrogen cycling is still unclear, despite that these factors may govern the fate of methane and nitrogen in wetlands. Here, we evaluated the vertical distribution of DAMO bacteria and archaea in soil layers along with the potential interactions among populations in the methane-coupled nitrogen cycling microbial community of Tibetan freshwater wetlands. A combination of molecular biology, stable isotope tracer technology, and microbial bioinformatics was used to evaluate these interrelated dynamics. The abundances and potential methane oxidation rates indicated that DAMO bacteria and archaea differentially occupy surface and subsurface soil layers, respectively. The inferred interactions between DAMO bacteria and nitrogen cycling microorganisms within their communities are complex, DAMO bacteria apparently achieve an advantage in the highly competitive environment of surface soils layers and occupy a specific niche in those environments. Conversely, the apparent relationships between DAMO archaea and nitrogen cycling microorganisms are relatively simple, wherein high levels of cooperation are inferred between DAMO archaea and nitrate-producing organisms in subsurface soils layers. These results suggest that the vertical distribution patterns of DAMO bacteria and archaea enable them to play significant roles in the methane oxidation activity of different soil layers and collectively form an effective methane filtration consortium.

Changes in the environmental microbiome in the Anthropocene

In addition to changes in climate, land cover, biodiversity, and chemical composition, human activity is also inducing great changes in the microbial world. These changes are profoundly affecting the biogeochemical processes of the Earth, the global biology, and the human health, that is, they are influencing the sustainability of the Anthropocene.

Long-Term Stochasticity Combines With Short-Term Variability in Assembly Processes to Underlie Rice Paddy Sustainability

Revealing temporal patterns of community assembly processes is important for understanding how microorganisms underlie the sustainability of agroecosystem. The ancient terraced rice paddies at Longji provide an ideal platform to study temporal dynamics of agroecosystem sustainability due to their chronosequential records of soil physicochemistry and well-archived microbial information along 630-year rice cultivation. We used statistical null models to evaluate microbial assembly processes along the soil chronosequences of Longji rice paddies through time. Stochastic and deterministic assembly processes jointly governed microbial community composition within successional eras (less than 250 years), and within-era determinism was mainly driven by soil fertility and redox conditions alone or in combination. Conversely, across successional eras (i.e., over 300 years), stochasticity linearly increased with increasing duration between eras and was eventually predominant for the whole 630 years. We suggest that the impact of stochasticity vs. determinism on assembly is timescale-dependent, and we propose that the importance of stochastic assembly of microbial community at longer timescales is due to the gradual changes in soil properties under long-term rice cultivation, which in turn contribute to the sustainability of paddy ecosystem by maintaining a diverse community of microorganisms with multi-functional traits. In total, our results indicate that knowledge on the timescales at which assembly processes govern microbial community composition is key to understanding the ecological mechanisms generating agroecosystem sustainability.

RNA Stable Isotope Probing of Potential Feammox Population in Paddy Soil

Anaerobic ammonium oxidation coupled to iron reduction (Feammox) is a recently discovered pathway contributing to nitrogen loss in various ecosystems such as paddy soils and sediments. However, little is known about the microbes driving Feammox in an agricultural ecosystem. Here, we demonstrated the occurrence of Feammox in paddy soils of Southern China using a ¹⁵N isotopic tracing technique, and examined the microbial communities associated with Feammox using RNA based stable isotope probing (RNA-SIP) combined with Illumina sequencing. Feammox was detected in all collected soils with direct N₂ production as the dominant Feammox pathway. It was estimated that approximately 6.91% of the applied nitrogen fertilizers were lost through Feammox in the paddy soils. RNA-SIP results showed that the composition of enriched active microbial communities were dependent on soil properties, especially the soil pH and grain size. Geobacter were enriched in most soils across various properties. The abundance of enriched GOUTA19 were significantly higher in soils with low pH than those in soils with medium pH and high pH, and the relative abundance of active Nitrososphaeraceae and Pseudomonas only increased in soils with medium and high pH during 4-day of incubation. These results suggested Feammox is a ubiquitous and important process for N loss. Geobacter, GOUTA19, Nitrososphaeraceae and Pseudomonas were active during the incubation that favored Feammox and the growth of Feammox microbes, suggesting these microbes were potentially associated with Feammox in natural agricultural soils.

The gut microbiota of soil organisms show species-specific responses to liming

Liming is a common agronomic practice used for alleviating soil acidification to improve plant growth. However, it is still unclear how liming can affect the gut microbiota composition of soil fauna, and subsequently the nutrient cycling and litter decomposition mediated by soil fauna. In the present study the effect of liming on the gut microbiota of two types of soil fauna, Folsomia candida, and Enchytraeus crypticus was investigated by using 16S rRNA gene high-throughput sequencing. The results revealed that there are differences between the gut microbial communities of the two types of soil fauna as well as between the gut microbiome of the soil fauna and the surrounding soil. Enterobacteriaceae and Bacillaceae were the predominant families in the gut microbiota of E. crypticus, while Rickettsiaceae and Moraxellaceae were the predominant families in the gut microbiota of F. candida. Liming affected the gut microbiota of E. crypticus at both the taxonomical and core microbiota level. The gut microbiota of F. candida was not affected by liming. Structural equation models suggest that 97% of the variation in the E. crypticus gut microbiota could be explained by liming-induced changes in soil properties and the soil microbial community. The indirect effects of liming, caused by a shift in the soil microbial community, contributed more in reshaping the gut microbiota of E. crypticus than the direct effects of the changed soil properties did. These findings suggest that the effects of liming on the gut microbiota composition in soil fauna are species-specific and are likely dependent on the response of the host to changes in soil properties and the soil microbial community.

Phytolith assemblage analysis for the identification of rice paddy

The rice arable system is of importance to both society and the environment. The emergence of rice paddies was a crucial step in the transition from pre-domestic cultivation to systematic land use and management. However, many aspects of the formation of rice farming systems remain unclear. An important reason is the lack of reliable methods for identifying early rice paddies. One possible means of remedying this knowledge deficit is through analysis of phytolith assemblages, which are closely related to their parent plant communities. In this study, phytolith assemblages from 27 surface soil samples from wild rice fields, 91 surface soil samples from modern rice paddies, and 50 soil samples from non-rice fields were analysed to establish a discriminant function. This discriminant function enabled classification of 89.3% of the samples into appropriate groups. Further, the results suggested that phytolith assemblages can be used to identify rice fields and differentiate between wild rice fields and domesticated rice fields. The method was demonstrated to be an effective way of utilising the large amounts of unidentifiable phytoliths discovered at archaeological sites to provide a modern analogue that may be a valuable key to unlocking the past.

Chronosequencing methanogenic archaea in ancient Longji rice Terraces in China

Chronosequences of ancient rice terraces serve as an invaluable archive for reconstructions of historical human-environment interactions. Presently, however, these reconstructions are based on traditional soil physico-chemical properties. The microorganisms in palaeosols have been unexplored. We hypothesized that microbial information can be used as an additional proxy to complement and consolidate archaeological interpretations. To test this hypothesis, the palaeoenvironmental methanogenic archaeal DNA in Longji Terraces, one of the famous ancient terraces in China, dating back to the late Yuan Dynasty (CE 1361-1406), was chronosequenced by high-throughput sequencing. It was found that the methanogenic archaeal abundance, diversity and community composition were closely associated with the 630years of rice cultivation and in line with changes in multi-proxy data. Particularly, the centennial- and decadal-scale influences of known historical events, including social turbulences (The Taiping Rebellion, CE 1850-1865), palaeoclimate changes (the Little Ice Age) and recorded natural disasters (earthquakes and inundation), on ancient agricultural society were clearly echoed in the microbial archives as variations in alpha and beta diversity. This striking correlation suggests that the microorganisms archived in palaeosols can be quantitatively and qualitatively analyzed to provide an additional proxy, and palaeo-microbial information could be routinely incorporated in the toolkit for archaeological interpretation.