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The mechanisms underlying community assembly and promoting temporal succession are often overlooked in microbial ecology. Here, we studied an undisturbed salt marsh chronosequence, spanning over a century of ecosystem development, to understand bacterial succession in soil. We used 16S rRNA gene-based quantitative PCR to determine bacterial abundance and multitag 454 pyrosequencing for community composition and diversity analyses. Despite 10-fold lower 16S rRNA gene abundances, the initial stages of soil development held higher phylogenetic diversities than the soil at late succession. Temporal variations in phylogenetic β-diversity were greater at initial stages of soil development, possibly as a result of the great dynamism imposed by the daily influence of the tide, promoting high immigration rates. Allogenic succession of bacterial communities was mostly driven by shifts in the soil physical structure, as well as variations in pH and salinity, which collectively explained 84.5% of the variation concerning community assemblage. The community assembly data for each successional stage were integrated into a network co-occurrence analysis, revealing higher complexity at initial stages, coinciding with great dynamism in turnover and environmental variability. Contrary to a spatial niche-based perspective of bacterial community assembly, we suggest temporal niche partitioning as the dominant mechanism of assembly (promoting more phylotype co-occurrence) in the initial stages of succession, where continuous environmental change results in the existence of multiple niches over short periods of time.

Decomposition is a dynamic ecological process dependent upon many factors such as environment, climate, and bacterial, insect, and vertebrate activity in addition to intrinsic properties inherent to individual cadavers. Although largely attributed to microbial metabolism, very little is known about the bacterial basis of human decomposition. To assess the change in bacterial community structure through time, bacterial samples were collected from several sites across two cadavers placed outdoors to decompose and analyzed through 454 pyrosequencing and analysis of variable regions 3–5 of the bacterial 16S ribosomal RNA (16S rRNA) gene. Each cadaver was characterized by a change in bacterial community structure for all sites sampled as time, and decomposition, progressed. Bacteria community structure is variable at placement and before purge for all body sites. At bloat and purge and until tissues began to dehydrate or were removed, bacteria associated with flies, such as Ignatzschineria and Wohlfahrtimonas , were common. After dehydration and skeletonization, bacteria associated with soil, such as Acinetobacter , were common at most body sites sampled. However, more cadavers sampled through multiple seasons are necessary to assess major trends in bacterial succession.

As an exotic plant species, Spartina alterniflora seriously threatens native ecosystem function in Chinese coastal regions. Unveiling the dynamics of soil bacteria community during its invasion is essential for a better understanding of related biogeochemical processes, while the shift in soil bacterial community over invasive time remains unclear. A short-term chronosequence was identified to assess the impacts of Spartina alterniflora invasion on soil nutrients and bacterial community composition and structure (using 16S rRNA gene high-throughput sequencing) over the time of invasion (i.e., (1) at least 10 years, (2) nearly 5 years, (3) less than 2 years, and (4) in native salt marshes or 0 years) in the Yellow River Estuary. The results exhibited an orderly change in the soil physicochemical properties and bacterial community composition over the invasion time. Soil pH showed a significant decrease with the accumulation of soil organic matter (SOM), whereas soil nutrients such as soil dissolved organic carbon (DOC), total nitrogen (TN), nitrate (NO₃-), ammonium (NH₄⁺), K⁺, and Mg²⁺ were generally increased with the age of the invasion. The number of operational taxonomic units (OTUs, 97% similarity level) exhibited a decreasing trend, which suggested a decline in bacterial diversity with the invasion age. The dominant groups at the phylum level were Proteobacteria, Bacteroidetes, Chloroflexi, Acidobacteria, and Gemmatimonadetes (the sum of relative abundance was > 70% across all samples). The relative abundances of Chloroflexi and Gemmatimonadetes steadily decreased, while the abundance of Bacteroidetes significantly increased with the plant invasion. The distribution pattern of the soil bacteria was clearly separated according to the principal coordinate analysis (PCoA) and canonical correspondence analysis (CCA) in native and invaded salt marshes. The variation in the soil bacterial community was tightly associated with the soil physicochemical properties (Mantel test, P < 0.05). Variance partitioning analysis (VPA) showed that plant traits explained 4.95% of the bacterial community variation, and soil variables explained approximately 26.96% of the variation. Network analysis also revealed that plant invasion strengthens the interaction among soil bacterial communities. Overall, our findings highlight the bacterial community succession during the Spartina alterniflora invasion in coastal salt marsh soils, which can provide insight regarding the association between soil development and invasive plant.

Microbial communities are important for high composting efficiency and good quality composts. This study was conducted to compare the changes of physicochemical and bacterial characteristics in composting from different raw materials, including chicken manure (CM), duck manure (DM), sheep manure (SM), food waste (FW), and vegetable waste (VW). The role and interactions of core bacteria and their contribution to maturity in diverse composts were analyzed by advanced bioinformatics methods combined sequencing with co-occurrence network and structural equation modeling (SEM). Results indicated that there were obviously different bacterial composition and diversity in composting from diverse sources. FW had a low pH and different physiochemical characteristics compared to other composts but they all achieved similar maturity products. Redundancy analysis suggested total organic carbon, phosphorus, and temperature governed the composition of microbial species but key factors were different in diverse composts. Network analysis showed completely different interactions of core bacterial community from diverse composts but Thermobifida was the ubiquitous core bacteria in composting bacterial network. Sphaerobacter and Lactobacillus as core genus were presented in the starting mesophilic and thermophilic phases of composting from manure (CM, DM, SM) and municipal solid waste (FW, VW), respectively. SEM indicated core bacteria had the positive, direct, and the biggest (> 80%) effects on composting maturity. Therefore, this study presents theoretical basis to identify and enhance the core bacteria for improving full-scale composting efficiency facing more and more organic wastes.

Understanding plant litter decomposition in broad-leaved forests is important because it influences the geochemical cycles of nutrients and represents a vital link in the global carbon cycle. Bacteria play an important role in litter decomposition, especially late in the decomposition process, when they become abundant. In this paper, we investigate bacterial community composition and diversity during about 1 year of Quercus wutaishanica litter decomposition using a molecular approach, to fill the gaps in knowledge about bacterial communities during decomposition. The results showed that the phyla Proteobacteria (Alpha and Betaproteobacteria), Actinobacteria, Bacteroidetes, and Acidobacteria were the most dominant throughout the experiment. As decomposition progressed, a dynamic succession of community and diversity was observed for different decomposition periods. Decay stages and seasonal shifts occurred by successful replacement of copiotrophic bacterial groups such as Betaproteobacteria in the early stage. During the entire process of decomposition, litter decomposition selectively stimulated the relative abundance of Alphaproteobacteria (Sphingomonas, Rhizobium, and Methylobacterium) and Bacteroidetes, but reduced the abundance of Massilia (Betaproteobacteria), Acidobacteria, and Actinobacteria. Among the abiotic factors, litter N and P content was the main factor driving the succession of litter bacteria. These results indicate the changes in decomposition stages in terms of the bacterial groups and elucidate the microbial community underpinnings of nutrient cycling in forest ecosystems.

Kefir is a fermented beverage produced through the activity of its grains, which is constituted by lactic acid and acetic acid bacteria and yeasts. We studied the bacterial succession during multiple fermentation of Argentinian kefir in brown sugar, purified molasses or high-test molasses, using 16S high-throughput sequencing. Firmicutes was dominant (up to 98% of total population) in grains and beverages made from various sugar substrates, except in high-test molasses beverage, which was dominated by Proteobacteria (up to 78% of total population). Major bacterial species in Firmicutes were Liquorilactobacillus nagelii, Lentilactobacillus hilgardii/diolivorans and Lacticaseibacillus casei/paracasei, which are active in lactic acid fermentation. Proteobacteria comprised Acetobacter lovaniensis and Gluconobacter oxydans/roseus as major species, which are presumably responsible for the acetic acid formation in sugary kefir beverages. Bacteria differ in abundance depending on the sugar type, as revealed by the competitive dominances between L. nagelii and A. loveniensis. Purified molasses led to scarce acetic acid bacteria during fermentation, indicating that it is not a suitable substrate for their growth. Our results suggest that acetic acid (and/or ethanol) in sugary kefir modulates the succession and dominance of specific lactic acid bacteria. This study will provide valuable information for designing more sophisticated non-dairy fermented beverages with stable microbial properties.

Aquatic decomposition, as a forensic discipline, has been largely under-investigated as a consequence of the highly complex and influential variability of the water environment. The limitation to the adaptability of scenario specific results justifies the necessity for experimental research to increase our understanding of the aquatic environment and the development of post-mortem submersion interval (PMSI) methods of estimation. This preliminary research aims to address this contextual gap by assessing the variation in the bacterial composition of aquatic biofilms as explained by water parameter measurements over time, associated with clothed and bare decomposing remains. As part of three field investigations, a total of 9 still-born piglets (n = 3, per trial) were used as human analogues and were submerged bare or clothed in either natural cotton or synthetic nylon. Changes in the bacterial community composition of the water surrounding the submerged remains were assessed at 4 discrete time points post submersion (7, 14, 21 and 28 days) by 16 S rRNA gene Next Generation Sequencing analysis and compared to coinciding water parameter measurements (i.e. conductivity, total dissolved solids (TDS), salinity, pH, and dissolved oxygen (DO)). Bacterial diversity was found to change over time and relative to clothing type, where significant variation was observed between synthetic nylon samples and bare/cotton samples. Seasonality was a major driver of bacterial diversity, where substantial variation was found between samples collected in early winter to those collected in mid - late winter. Water parameter measures of pH, salinity and DO were identified to best explain the global bacterial community composition and their corresponding dynamic trajectory patterns overtime. Further investigation into bacterial community dynamics in accordance with varying environmental conditions could potentially lead to the determination of influential extrinsic factors that may drive bacterial activity in aquatic decomposition. Together with the identification of potential bacterial markers that complement the different stages of decomposition, this may provide a future approach to PMSI estimations. •Clothing and clothing type have considerable impact on the global variation of decomposer aquatic bacterial communities.•Environmental variables including salinity, dissolved oxygen and pH drive bacterial assemblages of submerged remains.•Similar trends in Proteobacteria: Bacteroidota ratios indicate this could be used as a biomarker for estimating PMSI.•Differences in daily temperature highs and lows may have influence on the diversity of aquatic bacterial communities.

Multicellular organisms and their microbiomes can have a restricted and enduring relationship, sometimes reflected in their phylogenies, called phylosymbiosis. However, in some organisms, such as freshwater zooplankton, these relationships appear to be more flexible and more easily influenced by the environment. Here, we analysed the microbiome of a freshwater flatworm, Stenostomum leucops and sequenced the 16S RNA gene of the microbiota of a strain that was maintained in the laboratory for 12 years. This strain underwent four different cultivation conditions over the past 6 years, and the microbiome was characterised for each of these conditions. In addition, the microbiome of a wild S. leucops population was analysed. The microbiomes were highly variable between populations (Shannon index ranging from 0.26 to 2.06). It was not possible to determine a core microbiome, although Bacillus, Pseudomonas and Ralstonia were the predominant bacteria in populations under stable conditions. Under culture conditions where the water was contaminated with iron, Rhodoferax ferrireducens, a bacterium involved in iron reduction, was the predominant species. Our results are consistent with other studies on freshwater zooplankton. The microbiomes were very flexible and were influenced by the environment.

Anthropogenic eutrophication continuously degrades aquatic ecosystems and has led to a high frequency of massive cyanobacterial blooms in Taihu Lake since 1980. After bloom-forming cyanobacteria begin to disappear, substantial cyanobacterial scum accumulates and is degraded by microorganisms along the lakeshore. Several studies have revealed that cyanobacterial decomposition alters bacterial composition. However, the differences in responses among free-living and particle-attached bacteria to lake microbial community succession and the transition mechanism from one life strategy to another during cyanobacterial biomass and cyanobacteria-derived dissolved organic matter degradation remain unclear. This study investigated the microbial dynamics of cyanobacterial organic matter degradation over 61 days and revealed that complex interactions between particle-attached bacteria and cyanobacterial organic matter resulted in stage-specific changes in the chemical properties of water and a significant succession of the particle-attached bacterial community structure. As cyanobacteria biomass decayed, partial particle-attached bacteria transitioned into free-living bacteria. Successive free-living and particle-attached bacterial communities play important roles in driving dynamic variations in the chemical properties of water. This study provides new insights into the ecological processes and mechanisms governing the shift in bacterial community assembly between free-living and particle-attached bacteria during the post-bloom period in the Lake Taihu watershed.