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Vegetation restoration is crucial for improving the ecological environment of mining areas, which could promote the development of reconstructed soil, thus regulating biogeochemical cycles, and exerting ecosystem functions. Therefore, it is essential and necessary to conduct in-depth research on the impact of vegetation restoration on soil microbial communities in open-pit mining areas. In this study, surface soil samples were collected from six typical reclamation plots, including bare land (CK), Medicago sativa (GL), Hippophae rhamnoides (BL), Pinus tabulaeformis (CF), Populus tomentosa (BF), and Populus tomentosa + Pinus tabulaeformis (MF), located in the eastern waste dump of Heidaigou mining area of Zhungeer Banner, Inner Mongolia. High throughput sequencing, co-occurrence networks, and correlation analysis were used to explore the influential mechanism of vegetation types on soil abundant, rare bacterial and fungal community structural composition and diversity. Results showed that ① there were significant differences in the effects of different vegetation restoration types on soil physicochemical properties and enzyme activity (P

Stable bacterial communities are essential for maintaining soil functions. However, the role of abundant and rare bacterial taxa in maintaining bacterial community stability remains controversial. To explore the relationship between abundant and rare taxa and bacterial community stability, we used high‐throughput sequencing technology and molecular ecological networks to characterize the distribution of abundant and rare bacterial taxa under different nitrogen (N) fertilization rates (0, 150, 200, and 250 kg N hm−2). Our findings revealed that rare taxa had much higher Simpson's diversity index values than abundant taxa. Moreover, rare taxa Simpson's diversity decreased with increasing N application, while bacterial community differences (Bray–Curtis distance dissimilarity) increased (i.e., bacterial community stability decreased with increasing N application). The network topology showed that rare sub‐communities had higher modularity and a greater proportion of positive links than abundant taxa. The rare bacterial Simpson's diversity was significantly and negatively correlated with bacterial community differences, no correlation occurred between abundant bacterial Simpson's diversity and bacterial community differences. This study underscores the importance of rare species in maintaining bacterial community stability. Consequently, when optimizing agricultural management practices to ensure the stability of bacterial communities and soil functions, it is crucial not only to concentrate consider the roles of abundant species involved in nutrient cycling but also to give greater consideration to the role of rare taxa. [ABSTRACT FROM AUTHOR]

Introduction: The pivotal roles of both abundant and rare bacteria in ecosystem function are widely acknowledged. Despite this, the diversity elevational patterns of these two bacterial taxa in different seasons and influencing factors remains underexplored, especially in the case of rare bacteria. Methods: Here, a metabarcoding approach was employed to investigate elevational patterns of these two bacterial communities in different seasons and tested the roles of soil physico-chemical properties in structuring these abundant and rare bacterial community. Results and discussion: Our findings revealed that variation in elevation and season exerted notably effects on the rare bacterial diversity. Despite the reactions of abundant and rare communities to the elevational gradient exhibited similarities during both summer and winter, distinct elevational patterns were observed in their respective diversity. Specifically, abundant bacterial diversity exhibited a roughly U-shaped pattern along the elevation gradient, while rare bacterial diversity increased with the elevational gradient. Soil moisture and N:P were the dominant factor leading to the pronounced divergence in elevational distributions in summer. Soil temperature and pH were the key factors in winter. The network analysis revealed the bacteria are better able to adapt to environmental fluctuations during the summer season. Additionally, compared to abundant bacteria, the taxonomy of rare bacteria displayed a higher degree of complexity. Our discovery contributes to advancing our comprehension of intricate dynamic diversity patterns in abundant and rare bacteria in the context of environmental gradients and seasonal fluctuations. [ABSTRACT FROM AUTHOR]

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Numerous rare species coexist with a few abundant species in microbial communities and together play an essential role in riparian ecosystems. Relatively little is understood, however, about the nature of assembly processes of these communities and how they respond to a fluctuating environment. In this study, drivers controlling the assembly of abundant and rare subcommunities for bacteria and archaea in a riparian zone were determined, and their resulting patterns on these processes were analyzed. Abundant and rare bacteria and archaea showed a consistent variation in the community structure along the riparian elevation gradient, which was closely associated with flooding frequency. The community assembly of abundant bacteria was not affected by any measured environmental variables, while soil moisture and ratio of submerged time to exposed time were the two most decisive factors determining rare bacterial community. Assembly of abundant archaeal community was also determined by these two factors, whereas rare archaea was significantly associated with soil carbon–nitrogen ratio and total carbon content. The assembly process of abundant and rare bacterial subcommunities was driven respectively by dispersal limitation and variable selection. Undominated processes and dispersal limitation dominated the assembly of abundant archaea, whereas homogeneous selection primarily driven rare archaea. Flooding may therefore play a crucial role in determining the community assembly processes by imposing disturbances and shaping soil niches. Overall, this study reveals the assembly patterns of abundant and rare communities in the riparian zone and provides further insight into the importance of their respective roles in maintaining a stable ecosystem during times of environmental perturbations. [ABSTRACT FROM AUTHOR]

Karst rivers are highly susceptible to environmental disturbance due to their robust hydraulic connectivity. However, current knowledge of the mechanisms that regulate the assembly of bacterial and protistan subcommunities in river ecosystems, particularly in karst regions, is limited. By employing 16S and 18S rRNA gene amplicon sequencing, we explored how the diversities and assembly of abundant and rare bacterial and protistan subcommunities adapt to the local environmental variables in a karst river. Both bacterial and protistan rare subcommunities in karst river environments showed a similar biogeography to their abundant subcommunities. Also, a significant distance-decay pattern was observed in all components of the bacterial and protistan subcommunities along the Chishui River, with the rare subcommunities showing a more pronounced distance-decay pattern compared to the abundant subcommunities. Except protist rare subcommunity, the abundant and rare bacterial and abundant protistan subcommunities were strongly structured by the dispersal limitation processes rather than heterogeneous selection. Either bacteria or temperature, elevation and conductivity were the primary drivers for both abundant and rare subcommunities. Additionally, our results suggested that the rare subcommunities contribute significantly to the persistence and stability of microbial networks in the Chishui River, as they exhibited a higher number of keystones compared to the abundant subcommunities. Overall, our study revealed that in the karst river ecosystem, abundant bacterial subcommunities had a higher potential for environmental adaptation than rare bacterial and protistan subcommunities and identified the factors that moderate their assembly processes.

Background: Appendicitis is a frequent condition, with peak incidences in the second decade of life. Its pathogenesis is under debate, but bacterial infections are crucial, and antibiotic treatment remains essential. Rare bacteria are accused of causing complications, and various calculated antibiotics are propagated, yet there is no comprehensive microbiological analysis of pediatric appendicitis. Here we review different pre-analytic pathways, identify rare and common bacterial pathogens and their antibiotic resistances, correlate clinical courses, and evaluate standard calculated antibiotics in a large pediatric cohort. Method: We reviewed 579 patient records and microbiological results of intraoperative swabs in standard Amies agar media or fluid samples after appendectomies for appendicitis between May 2011 and April 2019. Bacteria were cultured and identified via VITEK 2 or MALDI-TOF MS. Minimal inhibitory concentrations were reevaluated according to EUCAST 2022. Results were correlated to clinical courses. Results: Of 579 analyzed patients, in 372 patients we got 1330 bacterial growths with resistograms. 1259 times, bacteria could be identified to species level. 102 different bacteria could be cultivated. 49% of catarrhal and 52% of phlegmonous appendices resulted in bacterial growth. In gangrenous appendicitis, only 38% remained sterile, while this number reduced to 4% after perforation. Many fluid samples remained sterile even when unsterile swabs had been taken simultaneously. 40 common enteral genera were responsible for 76.5% of bacterial identifications in 96.8% of patients. However, 69 rare bacteria were found in 187 patients without specifically elevated risk for complications. Conclusion: Amies agar gel swabs performed superior to fluid samples and should be a standard in appendectomies. Even catarrhal appendices were only sterile in 51%, which is interesting in view of a possible viral cause. According to our resistograms, the best in vitro antibiotic was imipenem with 88.4% susceptible strains, followed by piperacillin-tazobactam, cefuroxime with metronidazole, and ampicillin-sulbactam to which only 21.6% of bacteria were susceptible. Bacterial growths and higher resistances correlate to an elevated risk of complications. Rare bacteria are found in many patients, but there is no specific consequence regarding antibiotic susceptibility, clinical course, or complications. Prospective, comprehensive studies are needed to further elicit pediatric appendicitis microbiology and antibiotic treatment. [ABSTRACT FROM AUTHOR]

Introduction: The diagnosis of Mycoplasma periprosthetic joint infection (PJI) is rather difficult due to its rarity and difficult in isolation, there are not standardized diagnostic procedure for Mycoplasma PJI presently. This study aimed to reported a metagenomic next-generation sequencing (mNGS)-based diagnostic strategy for Mycoplasma PJI. Methods: In the present study, we have reported the largest number of Mycoplasma PJI that were precisely diagnosed by mNGS and verified by optimized microbial culture methods and (or) 16S PCR polymerase chain reaction (PCR). Results: The positive rate of optimized microbial culture methods and 16S PCR in the detection of Mycoplasma PJI was 57.14% and 71.43%, respectively. The infections were well controlled by targeted treatment in all cases. Conclusion: The standardized and optimized procedure based on mNGS presented in this study is useful for the diagnosis of Mycoplasma PJI, which might also be provided as a novel diagnostic strategy for rare bacterial PJI. [ABSTRACT FROM AUTHOR]

BackgroundAppendicitis is a frequent condition, with peak incidences in the second decade of life. Its pathogenesis is under debate, but bacterial infections are crucial, and antibiotic treatment remains essential. Rare bacteria are accused of causing complications, and various calculated antibiotics are propagated, yet there is no comprehensive microbiological analysis of pediatric appendicitis. Here we review different pre-analytic pathways, identify rare and common bacterial pathogens and their antibiotic resistances, correlate clinical courses, and evaluate standard calculated antibiotics in a large pediatric cohort.MethodWe reviewed 579 patient records and microbiological results of intraoperative swabs in standard Amies agar media or fluid samples after appendectomies for appendicitis between May 2011 and April 2019. Bacteria were cultured and identified via VITEK 2 or MALDI-TOF MS. Minimal inhibitory concentrations were reevaluated according to EUCAST 2022. Results were correlated to clinical courses.ResultsOf 579 analyzed patients, in 372 patients we got 1330 bacterial growths with resistograms. 1259 times, bacteria could be identified to species level. 102 different bacteria could be cultivated. 49% of catarrhal and 52% of phlegmonous appendices resulted in bacterial growth. In gangrenous appendicitis, only 38% remained sterile, while this number reduced to 4% after perforation. Many fluid samples remained sterile even when unsterile swabs had been taken simultaneously. 40 common enteral genera were responsible for 76.5% of bacterial identifications in 96.8% of patients. However, 69 rare bacteria were found in 187 patients without specifically elevated risk for complications.ConclusionAmies agar gel swabs performed superior to fluid samples and should be a standard in appendectomies. Even catarrhal appendices were only sterile in 51%, which is interesting in view of a possible viral cause. According to our resistograms, the best in vitro antibiotic was imipenem with 88.4% susceptible strains, followed by piperacillin-tazobactam, cefuroxime with metronidazole, and ampicillin-sulbactam to which only 21.6% of bacteria were susceptible. Bacterial growths and higher resistances correlate to an elevated risk of complications. Rare bacteria are found in many patients, but there is no specific consequence regarding antibiotic susceptibility, clinical course, or complications. Prospective, comprehensive studies are needed to further elicit pediatric appendicitis microbiology and antibiotic treatment.

Infective endocarditis remains a condition associated with high morbidity and mortality, regardless of advances in diagnosis and therapeutics. The etiology, microbiology, and epidemiology of infective endocarditis have changed in the last years, with healthcare-associated infective endocarditis being responsible for a myriad of cases. Raoultella planticola is rarely the cause of infective endocarditis. We present a 72-year-old Caucasian female with a history of mitral valve replacement for rheumatic valve disease two months before the current presentation, without any immunosuppressive pathologies, diagnosed with Raoultella planticola infective endocarditis. Long-drawn antibiotic treatment led to a full recovery with no evidence of recurrence or relapse. This report highlights the importance of a multimodal approach for the diagnosis of bacterial etiology, the importance of selection and duration of an appropriate antibiotic regimen, and the presence of a rare opportunistic bacteria that has proven pathogenicity in a wide range of organ systems, usually in patients with several risk factors.

Nitrogen (N) deep placement has been found to reduce N leaching and increase N use efficiency in paddy fields. However, relatively little is known how bacterial consortia, especially abundant and rare taxa, respond to N deep placement, which is critical for understanding the biodiversity and function of agricultural ecosystem. In this study, Illumina sequencing and ecological models were conducted to examine the diversity patterns and underlying assembly mechanisms of abundant and rare taxa in rice rhizosphere soil under different N fertilization regimes at four rice growth stages in paddy fields. The results showed that abundant and rare bacteria had distinct distribution patterns in rhizosphere samples. Abundant bacteria showed ubiquitous distribution; while rare taxa exhibited uneven distribution across all samples. Stochastic processes dominated community assembly of both abundant and rare bacteria, with dispersal limitation playing a more vital role in abundant bacteria, and undominated processes playing a more important role in rare bacteria. The N deep placement was associated with a greater influence of dispersal limitation than the broadcast N fertilizer (BN) and no N fertilizer (NN) treatments in abundant and rare taxa of rhizosphere soil; while greater contributions from homogenizing dispersal were observed for BN and NN in rare taxa. Network analysis indicated that abundant taxa with closer relationships were usually more likely to occupy the central position of the network than rare taxa. Nevertheless, most of the keystone species were rare taxa and might have played essential roles in maintaining the network stability. Overall, these findings highlighted that the ecological mechanisms and co-occurrence patterns of abundant and rare bacteria in rhizosphere soil under N deep placement.

Revealing the ecological patterns of abundant and rare microbial subcommunities in rhizosphere of cultivated plant is critical for understanding plant–microbe interactions and the formation of functionally important rhizosphere microbiome. Based on rhizodeposit support effects and colonization priority effects, the present study outlined two disparate hypotheses predicting the more deterministic assembly of abundant (the “dominance-determinism” hypothesis) and rare subcommunities (the “rare-determinism” hypothesis), respectively. These hypotheses were tested using bacterial and fungal subcommunities in the rhizosphere of three cultivated Panax species (P. ginseng, P. quinquefolium, and P. notoginseng). In each plant species, the abundant and rare taxa exhibited different patterns of distribution and composition, but similar edaphic factors could explain their phylogenetic community variations. Network analysis indicated that the abundant taxa located in more central positions than the rare taxa, and the negative links mainly exhibited between abundant and rare taxa. Null model showed that stochastic and deterministic processes dominated the assembly of abundant (determinism: 11.97–45.30 %) and rare (determinism: 67.24–96.30 %) subcommunities, respectively. In addition, almost all members of the rhizosphere abundant taxa (> 89 %) were also highly abundant in corresponding bulk soil. Among the three Panax species, the rare taxa exhibited stronger taxonomic overlap and phylogenetic similarity compared to the abundant taxa. These results indicate that the assembly of abundant subcommunities in Panax rhizosphere is highly stochastic and may relate to the priority effects, whereas the rare taxa tend to be the results of plant selection and exhibit potentially evolutionary conservatism.

Rare bacteria in rhizospheres from natural watermelon vs chimeric watermelon were investigated to understand the rare rhizobacteria assembling processes along with plant development and effects of rare species on functional stability. Over 80% of the total OTUs were defined as rare taxa (i.e., transient, permanent, and conditionally rare) in the rhizosphere. Among these three rarities, transient rare taxa possessed the highest richness, while the conditionally rarity displayed the largest variations along growth stages and exhibited the greatest deterministic process for assembling. Pairs of conditionally rare taxa with high asynchrony and similar functional potentials were identified in the rhizobacterial communities. This suggests the functional stability of the rhizosphere through functional redundancy. The number of pairs within the rhizosphere of chimeric plant was ~ two fold higher than that of natural watermelon, which illustrated that chimeric plants can stabilize rhizospheric functions. [ABSTRACT FROM AUTHOR]

Bacteria are vital components of lake systems, driving a variety of biogeochemical cycles and ecosystem services. Bacterial communities have been shown to have a skewed distribution with a few abundant species and a large number of rare species. The contribution of environmental processes or geographic distance in structuring these components is uncertain. The discrete nature of lakes provides an ideal test case to investigate microbial biogeographical patterns. In the present study, we used 16S rRNA gene metabarcoding to examine the distribution patterns on local and regional scales of abundant and rare planktonic bacteria across 167 New Zealand lakes covering broad environmental gradients. Only a few amplicon sequence variants (ASVs) were abundant with a higher proportion of rare ASVs. The proportion of locally abundant ASVs was negatively correlated with the percentage of high productivity grassland in the catchment and positively with altitude. Regionally rare ASVs had a restricted distribution and were only found in one or a few lakes. In general, regionally abundant ASVs had higher occupancy rates, although there were some with restricted occupancy. Environmental processes made a higher contribution to structuring the regionally abundant community, while geographic distances were more important for regionally rare ASVs. A better understanding of the processes structuring the abundance and distribution of bacterial communities within lakes will assist in understand microbial biogeography and in predicting how these communities might shift with environmental change. [ABSTRACT FROM AUTHOR]

Cryoconites harbor diverse microbial communities and are the metabolic hotspot in the glacial ecosystem. Glacial ecosystems are subjected to frequent climate disturbances such as precipitation (snowing), but little is known about whether microbial communities in cryoconite can maintain stability under such disturbance. Here, we investigated the bacterial community in supraglacial cryoconite before and after a snowfall event on the Laohugou Glacier (Tibetan Plateau), based on Illumina MiSeq sequencing of the 16S rRNA gene. Our results showed that the diversity of the microbial community significantly decreased, and the structure of the microbial community changed significantly after the disturbance of snowfall. This was partly due to the relative abundance increased of cold-tolerant bacterial taxa, which turned from rare into abundant sub-communities. After snowfall disturbance, the contribution of the deterministic process increased from 38 to 67%, which is likely due to the enhancement of environmental filtering caused by nitrogen limitation. These findings enhanced our understanding of the distribution patterns and assembly mechanisms of cryoconite bacterial communities on mountain glaciers. [ABSTRACT FROM AUTHOR]

Bacteria are vital components of lake systems, driving a variety of biogeochemical cycles and ecosystem services. Bacterial communities have been shown to have a skewed distribution with a few abundant species and a large number of rare species. The contribution of environmental processes or geographic distance in structuring these components is uncertain. The discrete nature of lakes provides an ideal test case to investigate microbial biogeographical patterns. In the present study, we used 16S rRNA gene metabarcoding to examine the distribution patterns on local and regional scales of abundant and rare planktonic bacteria across 167 New Zealand lakes covering broad environmental gradients. Only a few amplicon sequence variants (ASVs) were abundant with a higher proportion of rare ASVs. The proportion of locally abundant ASVs was negatively correlated with the percentage of high productivity grassland in the catchment and positively with altitude. Regionally rare ASVs had a restricted distribution and were only found in one or a few lakes. In general, regionally abundant ASVs had higher occupancy rates, although there were some with restricted occupancy. Environmental processes made a higher contribution to structuring the regionally abundant community, while geographic distances were more important for regionally rare ASVs. A better understanding of the processes structuring the abundance and distribution of bacterial communities within lakes will assist in understand microbial biogeography and in predicting how these communities might shift with environmental change.

Cryoconites harbor diverse microbial communities and are the metabolic hotspot in the glacial ecosystem. Glacial ecosystems are subjected to frequent climate disturbances such as precipitation (snowing), but little is known about whether microbial communities in cryoconite can maintain stability under such disturbance. Here, we investigated the bacterial community in supraglacial cryoconite before and after a snowfall event on the Laohugou Glacier (Tibetan Plateau), based on Illumina MiSeq sequencing of the 16S rRNA gene. Our results showed that the diversity of the microbial community significantly decreased, and the structure of the microbial community changed significantly after the disturbance of snowfall. This was partly due to the relative abundance increased of cold-tolerant bacterial taxa, which turned from rare into abundant sub-communities. After snowfall disturbance, the contribution of the deterministic process increased from 38 to 67%, which is likely due to the enhancement of environmental filtering caused by nitrogen limitation. These findings enhanced our understanding of the distribution patterns and assembly mechanisms of cryoconite bacterial communities on mountain glaciers.

There are differences in the environmental adaptability and regulation of nutrient cycling between abundant and rare bacterial communities during the development of planted forest ecosystems. In this study, we aimed to elucidate the relationships between the soil characteristics and the composition and diversity of abundant and rare bacteria across a chronosequence (i.e., 13-yr, 25-yr, 38-yr, 58-yr-old stands) of Pinus massoniana. Abundant bacterial OTUs, richness, and Shannon index showed a different variation with stand age compared with the rare taxa bacterial community. Both abundant and rare bacterial communities showed significant differences between the 13-yr and 25-yr-old stands, but were similar in the 38-yr and 58-yr-old stands. The dominant phyla were Acidobacteria, Proteobacteria, Chloroflexi, Actinobacteria, and Planctomycetes in both abundant and rare taxa. However, the same phylum of abundant and rare taxa was inconsistent across the four forest ages. Network analysis further demonstrated that rare taxa had a greater network scale and complexity than abundant taxa, which may contribute to buffering the environmental stress. The Mantel test showed that soil pH, nitrogen pool (i.e., MBN, NH4+, NAlkali), and enzyme activities were the key factors that were associated with the changes in abundant bacterial diversity and structure during the development of P. massoniana. However, more soil variables (i.e., pH, SW, MBN, NH4+, NAlkali, AP, nitrite reductase, and sucrase) regulated the rare bacterial communities. Our results indicate that rare taxa are important contributors to soil bacterial community diversity, and their community dynamics responded to changes in soil physicochemical properties significantly distinct from the abundant taxa. We suggest that future studies should focus more on the response of different taxa subcommunities, rather than on the community as a whole, when studying the changes in microbial community dynamics.

ABSTRACT Microbial communities commonly consist of a large number of rare taxa (RT) and few abundant taxa (AT), and it is important to identify the differences of the community assembly processes between RT and AT in response to environmental changes. However, the community assembly processes governing AT and RT in coastal wetland soils along an inundation gradient remain elusive. Here, an in situ mesocosm, with continuous inundation gradients and native mangrove Kandelia obovata or exotic cordgrass Spartina alterniflora, was established to determine the patterns and driving factors of community turnover and assembly processes of AT and RT. We found that RT exhibited a remarkably lower turnover rate than AT, and the niche breadth of RT was significantly narrower than that of AT. In comparison with AT, RT presented stronger phylogenetic signals for ecological preferences across environmental gradients. Null model analyses revealed that RT were more phylogenetically clustered and primarily governed by homogeneous selection, while AT were more overdispersed and dominated by dispersal limitation. Soil water content was the most decisive factor for community turnover and assembly processes of both AT and RT. Structural equation modeling analysis showed that RT were strongly associated with K. obovata biomass rather than S. alterniflora biomass, suggesting a strong relationship between RT and the growth of mangrove K. obovata. Overall, our study revealed distinct assembly processes of soil AT and RT communities in coastal wetlands, which is crucial for mechanistic understanding of the establishment and maintenance of soil microbial diversity in coastal wetlands under conditions of global environmental changes. IMPORTANCE Coastal wetlands are one of the important ecosystems that play a crucial role in the regulation of climate change. Rare taxa (RT) exist in one habitat along with abundant taxa (AT). In this study, we found that RT exhibited narrower niche breadth and stronger phylogenetic signals than AT. Null model analyses showed that RT were more phylogenetically clustered and primarily governed by homogeneous selection, while AT were more overdispersed and dominated by dispersal limitation. Revealing the differences in the community assembly processes between AT and RT in coastal wetlands is critical to understand the establishment and maintenance of soil microbial diversity in coastal wetlands with regard to environmental changes.

Introduction: The pivotal roles of both abundant and rare bacteria in ecosystem function are widely acknowledged. Despite this, the diversity elevational patterns of these two bacterial taxa in different seasons and influencing factors remains underexplored, especially in the case of rare bacteria., Methods: Here, a metabarcoding approach was employed to investigate elevational patterns of these two bacterial communities in different seasons and tested the roles of soil physico-chemical properties in structuring these abundant and rare bacterial community., Results and Discussion: Our findings revealed that variation in elevation and season exerted notably effects on the rare bacterial diversity. Despite the reactions of abundant and rare communities to the elevational gradient exhibited similarities during both summer and winter, distinct elevational patterns were observed in their respective diversity. Specifically, abundant bacterial diversity exhibited a roughly U-shaped pattern along the elevation gradient, while rare bacterial diversity increased with the elevational gradient. Soil moisture and N:P were the dominant factor leading to the pronounced divergence in elevational distributions in summer. Soil temperature and pH were the key factors in winter. The network analysis revealed the bacteria are better able to adapt to environmental fluctuations during the summer season. Additionally, compared to abundant bacteria, the taxonomy of rare bacteria displayed a higher degree of complexity. Our discovery contributes to advancing our comprehension of intricate dynamic diversity patterns in abundant and rare bacteria in the context of environmental gradients and seasonal fluctuations., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Wu, Hu, Guo, Li, Zhong and Cheng.)

Traditional cultivation approaches in microbiology are labor-intensive, low-throughput, and yield biased sampling of environmental microbes due to ecological and evolutionary factors. New strategies are needed for ample representation of rare taxa and slow-growers that are often outcompeted by fast-growers in cultivation experiments. Here we describe a microfluidic platform that anaerobically isolates and cultivates microbial cells in millions of picoliter droplets and automatically sorts them based on colony density to enhance slow-growing organisms. We applied our strategy to a fecal microbiota transplant (FMT) donor stool using multiple growth media, and found significant increase in taxonomic richness and larger representation of rare and clinically relevant taxa among droplet-grown cells compared to conventional plates. Furthermore, screening the FMT donor stool for antibiotic resistance revealed 21 populations that evaded detection in plate-based assessment of antibiotic resistance. Our method improves cultivation-based surveys of diverse microbiomes to gain deeper insights into microbial functioning and lifestyles.

Humic acid (HA) is widely used for soil quality improvement, yet little is known how bacterial communities, especially common and rare bacteria, respond to HA amendment, which is crucial to understand biodiversity and function in agroecosystem. Therefore, a manipulated microcosm experiment with a gradient of HA amendment was conducted to unveil this. The results showed that common and rare taxa had similar patterns in species richness, while rare taxa exhibited a higher turnover, which caused their higher structural dissimilarity. Common species with wider niche breadths were more strongly influenced by deterministic filtering when compared to rare taxa, which occupied narrow niches and were primarily controlled by stochastic processes. Generally, species with wider niche breadths were always more strongly influenced by deterministic selection. The analysis of predicted functions revealed that rare taxa occupied more unique predicted functional traits than common taxa, suggesting that rare taxa played a key role in maintaining the functional diversity. In addition, there was a significant positive correlation between species richness and predicted functional diversity in rare taxa rather than common taxa. Our findings highlight the distinct structural and predicted functional successions of common and rare bacteria in soil under HA amendment.

Humic acid (HA) is widely used for soil quality improvement, yet little is known how bacterial communities, especially common and rare bacteria, respond to HA amendment, which is crucial to understand biodiversity and function in agroecosystem. Therefore, a manipulated microcosm experiment with a gradient of HA amendment was conducted to unveil this. The results showed that common and rare taxa had similar patterns in species richness, while rare taxa exhibited a higher turnover, which caused their higher structural dissimilarity. Common species with wider niche breadths were more strongly influenced by deterministic filtering when compared to rare taxa, which occupied narrow niches and were primarily controlled by stochastic processes. Generally, species with wider niche breadths were always more strongly influenced by deterministic selection. The analysis of predicted functions revealed that rare taxa occupied more unique predicted functional traits than common taxa, suggesting that rare taxa played a key role in maintaining the functional diversity. In addition, there was a significant positive correlation between species richness and predicted functional diversity in rare taxa rather than common taxa. Our findings highlight the distinct structural and predicted functional successions of common and rare bacteria in soil under HA amendment. [ABSTRACT FROM AUTHOR]

Abstract Background In recent years, saprophytic bacteria have been emerging as potential human pathogens causing life-threatening infections in patients with malignancies. However, evidence is lacking concerning such bacteria, particularly in sub-Saharan countries. This study was designed to determine the spectrum and drug resistance profile of the rare bacterial pathogens causing bloodstream infections (BSIs) in febrile cancer patients at a referral hospital in Ethiopia. Methods Between December 2011 and June 2012, blood samples were collected from 107 patients with cancer in Tikur Anbessa hospital. Culturing was performed using the blood culture bottles and solid media and the microorganisms were identified using the gram staining and APINE identification kits (Biomerieux, France). The disk diffusion method was used for the antimicrobial susceptibility testing. Results Overall, 13 (12.2%) rare human pathogens were isolated from 107 adult febrile cancer patients investigated. Aeromonas hydrophilia species (a fermentative gram-negative rod) was the predominant isolate, 30.8% (4/13), followed by Chryseomonas luteola 15.4% (2/13), Sphignomonas poucimobilis 15.4% (2/13), and Pseudomonas fluorescens 15.4% (2/13). Of the nine isolates tested for a nine set of antibiotics, 89% were resistant to amoxicillin-clavulanic acid, ampicillin, and trimethoprim-sulphamethoxazole. Conclusions This study revealed the emergence of saprophytic bacteria as potential drug-resistant nosocomial pathogens in Ethiopian patients with cancer. As these pathogens are ubiquitous in the environment, infection prevention actions should be strengthened in the hospital and early diagnosis and treatment with appropriate antibiotics are warranted for those already infected.

High-throughput sequencing is commonly used to study soil microbial communities. However, different primers targeting different 16S rRNA hypervariable regions often generate different microbial communities and result in different values of diversity and community structure. This study determined the consequences of using two bacterial primers (338f/806r, targeting the V3–V4 region, and 520f/802r, targeting the V4 region) to assess bacterial communities in the soils of different land uses along a latitudinal gradient. The results showed that the variations in the soil bacterial diversity in different land uses were more evident based on the former pair. The statistical results showed that land use had no significant impact on soil bacterial diversity when primer pair 520f/802r was used. In contrast, when primer pair 338f/806r was used, the cropland and orchard soils had significantly higher operational taxonomic units (OTUs) and Shannon diversity index values than those of the shrubland and grassland soils. Similarly, the soil bacterial diversity generated by primer pair 338f/806r was significantly impacted by mean annual precipitation, soil total phosphorus (TP), soil total nitrogen (TN), and soil available phosphorus (AVP), while the soil bacterial diversity generated by primer pair 520f/802r showed no significant correlations with most of these environmental factors. Multiple regression models indicated that soil pH and soil organic carbon (SOC) shaped the soil bacterial community structure on the Loess Plateau regardless of what primer pair was used. Climatic conditions mainly affected the diversity of rare bacteria. Abundant bacteria are more sensitive than rare bacteria to environmental changes. Very little of the variation in the rare bacterial community was explained by environmental factors or geographic distance, suggesting that the communities of rare bacteria are unpredictable. The distributions of the abundant taxa were mainly determined by variations in environmental factors.

The assembly of the root-associated microbiome provides mutual benefits for the host plant and bacteria in soils. It is interesting how invasive plants interact with the local soil microbial community and establish the soil bacterial community in the endosphere of these plants in the short term. In this study, we compared the bacterial community in the rhizosphere with that in the root endosphere of an invasive plant, Ageratina adenophora , using high-throughput sequencing. The results showed that the roots of A. adenophora selectively accumulated the genera Clostridium and Enterobacter , which are rarely distributed in the rhizosphere. This selective accumulation caused a switch in the bacterial composition at the phylum level from Bacteroidetes predominant in the rhizosphere to Proteobacteria dominant in the root endosphere of A. adenophora. Our data indicated the potential existence of a highly conserved signal recognition in which hosts, either invasive or native, enrich the endosphere bacteria, such as Clostridium , Enterobacter , etc., from the rhizosphere. Moreover, the accumulated bacteria were physiologically and genetically different at the strain level and displayed distinct roles in growth between invasive and native plants. The assembly of the bacterial community in the roots may be an advantageous strategy for A. adenophora in competition with native plants. Unlabelled Image • Ageratina adenophora selectively accumulate bacteria from soil rare bacteria. • Bacteroidetes dominant in rhizobacteria but Proteobacteria dominant in endophytes. • The accumulated bacteria are different for plant growth at the strain level. [ABSTRACT FROM AUTHOR]

Introduction: Ten years after its introduction into clinical microbiology, MALDI-TOF mass spectrometry has become the standard routine identification tool for bacteria in most laboratories. The technology has accelerated analyses and improved the quality of results. The greatest significance has been observed for bacteria that were challenging to be identified by traditional methods. Areas covered: We searched in existing literature (Pubmed) for reports how MALDI-TOF MS has contributed to identification of rare and unknown bacteria from different groups. We describe how this has improved the diagnostics in different groups of bacteria. Reference patterns for strains which yet cannot be assigned to a known species even enable the search for related bacteria in studies as well as in routine diagnostics. MALDI-TOF MS can help to discover and investigate new species and their clinical relevance. It is a powerful tool in the elucidation of the bacterial composition of complex microbiota in culturomics studies. Expert opinion: MALDI-TOF MS has improved the diagnosis of bacterial infections. It also enables knowledge generation for prospective diagnostics. The term 'hard-to-identify' might only be rarely attributed to bacteria in the future. Novel applications are being developed, e.g. subspecies differentiation, typing, and antibiotic resistance testing which may further contribute to improved microbial diagnostics. [ABSTRACT FROM AUTHOR]

Elevational gradients are powerful 'natural laboratory' for testing the responses of microbes to geophysical influences. Microbial communities are normally composed of a few abundant and many rare taxa. Abundant and rare taxa play different ecological roles in kinds of environments, but how their diversity and composition patterns response to elevation gradients is still poorly elucidated. In this study, we investigated the elevational patterns of abundant and rare bacterial diversity and composition in a mountain stream from 712 to 3435 m at Gangrigabu Mountain on the Tibetan Plateau, China. Our results revealed abundant and rare bacteria had similar decreasing elevation trend of alpha diversity, and both of them showed a significant elevational distance-decay relationship. However, the turnover rate of the elevational distance-decay of rare bacteria was higher than that of abundant bacteria. The species-abundance distribution patterns of rare taxonomic composition were associated with the elevational gradient, while most of abundant bacterial clades did not display any relationships with elevation. Our results suggested that rare bacteria were more sensitive to changes in elevation gradient. [ABSTRACT FROM AUTHOR]

Microbial taxa range from being ubiquitous and abundant across space to extremely rare and endemic, depending on their ecophysiology and on different processes acting locally or regionally. However, little is known about how cosmopolitan or rare taxa combine to constitute communities and whether environmental variations promote changes in their relative abundances. Here we identified the Spatial Abundance Distribution (SpAD) of individual prokaryotic taxa (16S rDNA‐defined Operational Taxonomic Units, OTUs) across 108 globally‐distributed surface ocean stations. We grouped taxa based on their SpAD shape ("normal‐like"‐ abundant and ubiquitous; "logistic"‐ globally rare, present in few sites; and "bimodal"‐ abundant only in certain oceanic regions), and investigated how the abundance of these three categories relates to environmental gradients. Most surface assemblages were numerically dominated by a few cosmopolitan "normal‐like" OTUs, yet there was a gradual shift towards assemblages dominated by "logistic" taxa in specific areas with productivity and temperature differing the most from the average conditions in the sampled stations. When we performed the SpAD categorization including additional habitats (deeper layers and particles of varying sizes), the SpAD of many OTUs changed towards fewer "normal‐like" shapes, and OTUs categorized as globally rare in the surface ocean became abundant. This suggests that understanding the mechanisms behind microbial rarity and dominance requires expanding the context of study beyond local communities and single habitats. We show that marine bacterial communities comprise taxa displaying a continuum of SpADs, and that variations in their abundances can be linked to habitat transitions or barriers that delimit the distribution of community members. [ABSTRACT FROM AUTHOR]

Revealing the biogeographies and ecologies of rare and abundant microorganisms is crucial to understand ecosystem diversity and function. In this study, we investigated the biogeographic assemblies and ecological diversity patterns of rare and abundant bacteria in long-term oil-contaminated soils at intervals of 46-360 km by performing high-throughput sequencing of 16S r RNA genes. The results clearly revealed distinct distribution patterns for rare and abundant bacteria in soil samples. Rare taxa were unevenly distributed; however, abundant taxa were ubiquitous across all samples. Both rare and abundant subcommunities showed significant distance-decay relationships, and their assemblies were driven by different factors. The rare subcommunity primarily exhibited a spatially structured distribution (i.e., stochastic processes), while edaphic factors (i.e., deterministic processes) largely contributed to the structure of the abundant subcommunity. A network analysis revealed closer relationships between abundant bacteria and their heightened influence on other co-occurrences in the community compared with rare species. In conclusion, rare microbial taxa may play potential roles in maintaining ecosystem diversity, although they do not appear to be central to microbial networks. Abundant microbes are vital for microbial co-occurrences in oil-contaminated soils, and high relative abundance and ubiquitous distribution suggest potential roles in the degradation of organic pollutants. [ABSTRACT FROM AUTHOR]

Background: In recent years, saprophytic bacteria have been emerging as potential human pathogens causing life-threatening infections in patients with malignancies. However, evidence is lacking concerning such bacteria, particularly in sub-Saharan countries. This study was designed to determine the spectrum and drug resistance profile of the rare bacterial pathogens causing bloodstream infections (BSIs) in febrile cancer patients at a referral hospital in Ethiopia. Methods: Between December 2011 and June 2012, blood samples were collected from 107 patients with cancer in Tikur Anbessa hospital. Culturing was performed using the blood culture bottles and solid media and the microorganisms were identified using the gram staining and APINE identification kits (Biomerieux, France). The disk diffusion method was used for the antimicrobial susceptibility testing. Results: Overall, 13 (12.2%) rare human pathogens were isolated from 107 adult febrile cancer patients investigated. Aeromonas hydrophilia species (a fermentative gram-negative rod) was the predominant isolate, 30.8% (4/13), followed by Chryseomonas luteola 15.4% (2/13), Sphignomonas poucimobilis 15.4% (2/13), and Pseudomonas fluorescens 15.4% (2/13). Of the nine isolates tested for a nine set of antibiotics, 89% were resistant to amoxicillin-clavulanic acid, ampicillin, and trimethoprim-sulphamethoxazole. Conclusions: This study revealed the emergence of saprophytic bacteria as potential drug-resistant nosocomial pathogens in Ethiopian patients with cancer. As these pathogens are ubiquitous in the environment, infection prevention actions should be strengthened in the hospital and early diagnosis and treatment with appropriate antibiotics are warranted for those already infected. [ABSTRACT FROM AUTHOR]

Elucidating the driving forces behind the temporal dynamics of abundant and rare microbes is essential for understanding the assembly and succession of microbial communities. Here, we explored the successional trajectories and mechanisms of abundant and rare bacteria via soil-enrichment subcultures in response to various pollutants (phenanthrene, n -octadecane, and CdCl 2 ) using time-series Illumina sequencing datasets. The results reveal different successional patterns of abundant and rare sub-communities in eighty pollutant-degrading consortia and two original soil samples. A temporal decrease in α -diversity and high turnover rate for β -diversity indicate that deterministic processes are the main drivers of the succession of the abundant sub-community; however, the high cumulative species richness indicates that stochastic processes drive the succession of the rare sub-community. A functional prediction showed that abundant bacteria contribute primary functions to the pollutant-degrading consortia, such as amino acid metabolism, cellular responses to stress, and hydrocarbon degradation. Meanwhile, rare bacteria contribute a substantial fraction of auxiliary functions, such as carbohydrate-active enzymes, fermentation, and homoacetogenesis, which indicates their roles as a source of functional diversity. Our study suggests that the temporal succession of microbes in polluted microcosms is mainly associated with abundant bacteria rather than the high proportion of rare taxa. The major forces (i.e., stochastic or deterministic processes) driving microbial succession could be dependent on the low- or high-abundance community members in temporal microcosms with pollutants. [ABSTRACT FROM AUTHOR]

In agroecosystem soils, abundant and rare biospheres have coexisted, resulting in complex interactive systems. It has remained unclear how agricultural practices have impacted the assembly of abundant and rare bacteria within root-associated compartments. The response of abundant and rare bacteria to plastic film mulch (PM) was investigated on a fine-compartment scale from bulk soil to rhizoplane, based on an in-situ experiment. The results indicated that root-associated communities were reactive to root selection, with abundant taxa having a greater niche breadth than rare taxa. The results of SourceTracker and the reduction of niche breadths from bulk soil to rhizoplane emphasized the role of roots in bacterial recruitment, with PM exerting greater host selection pressure. The assembly of abundant taxa was primarily impacted by variable selection, whereas that of rare taxa was influenced by homogeneous selection. PM amplified the impact of deterministic and stochastic processes on abundant and rare taxa. In contrast to rare taxa, abundant taxa were more frequently located in the center of networks, and PM greatly strengthened co-occurrence. Several abundant operational taxonomy units (OTUs) reflected their roles in maintaining microbial co-occurrence as keystone species. While the stochastic assembly of rare taxa was closely related to crop yield at the community level. Overall, these findings demonstrated how agricultural practices have had an impact on soil microbial communities along with the fine-scale compartments. They have demonstrated that PM would be having a major impact on the assembly of abundant and rare root-associated bacteria in drylands. [Display omitted] • Root-associated abundant and rare taxa within fine-scale compartments were studied. • Distinct abundant and rare subcommunities were shaped by plastic film mulch (PM). • PM altered the recruitment and assembly process of abundant and rare subcommunities. • Root traits play a vital role in the assembly of abundant and rare subcommunities. • Rhizoplane under PM enriched abundant taxa with plant growth-promoting ability. [ABSTRACT FROM AUTHOR]

Introduction: The diagnosis of Mycoplasma periprosthetic joint infection (PJI) is rather difficult due to its rarity and difficult in isolation, there are not standardized diagnostic procedure for Mycoplasma PJI presently. This study aimed to reported a metagenomic next-generation sequencing (mNGS)-based diagnostic strategy for Mycoplasma PJI., Methods: In the present study, we have reported the largest number of Mycoplasma PJI that were precisely diagnosed by mNGS and verified by optimized microbial culture methods and (or) 16S PCR polymerase chain reaction (PCR)., Results: The positive rate of optimized microbial culture methods and 16S PCR in the detection of Mycoplasma PJI was 57.14% and 71.43%, respectively. The infections were well controlled by targeted treatment in all cases., Conclusion: The standardized and optimized procedure based on mNGS presented in this study is useful for the diagnosis of Mycoplasma PJI, which might also be provided as a novel diagnostic strategy for rare bacterial PJI., (Copyright © 2023 Cai, Ding, Chen, Chen, Huang, Zhang, Huang, Huang, Li, Zhang and Fang.)

• The assembly of abundant rhizosphere taxa is dominated by stochastic processes. • The rare subcommunities are mainly shaped by deterministic processes. • The abundant taxa locate in more central positions of the co-occurrence network. • Negative co-occurrence links are overrepresented by abundant–rare correlations. • The rare taxa show strong ecological similarity among distinct Panax species. Revealing the ecological patterns of abundant and rare microbial subcommunities in rhizosphere of cultivated plant is critical for understanding plant–microbe interactions and the formation of functionally important rhizosphere microbiome. Based on rhizodeposit support effects and colonization priority effects, the present study outlined two disparate hypotheses predicting the more deterministic assembly of abundant (the "dominance-determinism" hypothesis) and rare subcommunities (the "rare-determinism" hypothesis), respectively. These hypotheses were tested using bacterial and fungal subcommunities in the rhizosphere of three cultivated Panax species (P. ginseng , P. quinquefolium , and P. notoginseng). In each plant species, the abundant and rare taxa exhibited different patterns of distribution and composition, but similar edaphic factors could explain their phylogenetic community variations. Network analysis indicated that the abundant taxa located in more central positions than the rare taxa, and the negative links mainly exhibited between abundant and rare taxa. Null model showed that stochastic and deterministic processes dominated the assembly of abundant (determinism: 11.97–45.30 %) and rare (determinism: 67.24–96.30 %) subcommunities, respectively. In addition, almost all members of the rhizosphere abundant taxa (> 89 %) were also highly abundant in corresponding bulk soil. Among the three Panax species, the rare taxa exhibited stronger taxonomic overlap and phylogenetic similarity compared to the abundant taxa. These results indicate that the assembly of abundant subcommunities in Panax rhizosphere is highly stochastic and may relate to the priority effects, whereas the rare taxa tend to be the results of plant selection and exhibit potentially evolutionary conservatism. [ABSTRACT FROM AUTHOR]

Leclercia adecarboxylata is a motile Gram negative rod that is not often pathogenic in immunocompetent patients. We will present the first case report of a L. adecarboxylata in a pediatric patient with no systemic medical disease and present a detailed literature review. [ABSTRACT FROM AUTHOR]

• Diversities of abundant and rare taxa exhibited a similar response to cover crop. • Only the fungal subcommunities structures were affected by cover crop. • Assembly of abundant bacteria was affected by cover crop rather than growth period. • Assembly of abundant and rare fungi were not affected by growth period and cover crop. • The assembly processes of each subcommunity were driven by distinct soil factors. Soil microorganisms play key roles in agricultural ecosystems. However, little is known about their dynamic diversity patterns and community assembly processes, especially in the rare microbial biosphere in agriculture systems. In this study, we determined the responses of diversities and assembly processes of abundant and rare bacterial and fungal subcommunities to agricultural practice (i.e. cover crop) in a semiarid orchard soil by using 16S and ITS rRNA gene sequencing. We found that the community structures of abundant and rare taxa exhibited a similar response to cover crop or growth periods. Growth periods significantly changed the bacterial and fungal subcommunities structure. Only the fungal subcommunities structure was affected by cover crop. The community assembly of abundant and rare fungi was respectively dominated by stochastic process and deterministic process and less affected by cover crop and growth period. For abundant bacteria, the assembly process was dominated by heterogeneous and undominated processes, and the importance of heterogeneous selection process was increased by cover crop at setting and maturing period. The assembly process of rare bacterial community was dominated by a homogeneous selection and the relative importance of dispersal limitation was increased at maturing period. We also found that the assembly processes of abundant taxa were significantly related to the soil DON, NH 4 +-N, NO 3 –-N and pH, while the assembly processes of rare taxa were significantly related to the soil DOC, AP and SOC. Our results provide new insights into the formation of the microbial community in orchard soil under a cover crop, especially the seasonal succession of abundant and rare bacterial and fungal subcommunities. [ABSTRACT FROM AUTHOR]

Reports on the discovery of several novel microorganisms belonging to the minority group that could be isolated with enrichment culture for as long as two months. Examination of dynamic change in microbial flora with an oxygen electrode; Isolation of slow-growing bacteria; Homology with Bradyrhizobium japonicum.

High-throughput sequencing is commonly used to study soil microbial communities. However, different primers targeting different 16S rRNA hypervariable regions often generate different microbial communities and result in different values of diversity and community structure. This study determined the consequences of using two bacterial primers (338f/806r, targeting the V3–V4 region, and 520f/802r, targeting the V4 region) to assess bacterial communities in the soils of different land uses along a latitudinal gradient. The results showed that the variations in the soil bacterial diversity in different land uses were more evident based on the former pair. The statistical results showed that land use had no significant impact on soil bacterial diversity when primer pair 520f/802r was used. In contrast, when primer pair 338f/806r was used, the cropland and orchard soils had significantly higher operational taxonomic units (OTUs) and Shannon diversity index values than those of the shrubland and grassland soils. Similarly, the soil bacterial diversity generated by primer pair 338f/806r was significantly impacted by mean annual precipitation, soil total phosphorus (TP), soil total nitrogen (TN), and soil available phosphorus (AVP), while the soil bacterial diversity generated by primer pair 520f/802r showed no significant correlations with most of these environmental factors. Multiple regression models indicated that soil pH and soil organic carbon (SOC) shaped the soil bacterial community structure on the Loess Plateau regardless of what primer pair was used. Climatic conditions mainly affected the diversity of rare bacteria. Abundant bacteria are more sensitive than rare bacteria to environmental changes. Very little of the variation in the rare bacterial community was explained by environmental factors or geographic distance, suggesting that the communities of rare bacteria are unpredictable. The distributions of the abundant taxa were mainly determined by variations in environmental factors. [ABSTRACT FROM AUTHOR]

Microbial communities commonly consist of a large number of rare taxa (RT) and few abundant taxa (AT), and it is important to identify the differences of the community assembly processes between RT and AT in response to environmental changes. However, the community assembly processes governing AT and RT in coastal wetland soils along an inundation gradient remain elusive. Here, an in situ mesocosm, with continuous inundation gradients and native mangrove Kandelia obovata or exotic cordgrass Spartina alterniflora , was established to determine the patterns and driving factors of community turnover and assembly processes of AT and RT. We found that RT exhibited a remarkably lower turnover rate than AT, and the niche breadth of RT was significantly narrower than that of AT. In comparison with AT, RT presented stronger phylogenetic signals for ecological preferences across environmental gradients. Null model analyses revealed that RT were more phylogenetically clustered and primarily governed by homogeneous selection, while AT were more overdispersed and dominated by dispersal limitation. Soil water content was the most decisive factor for community turnover and assembly processes of both AT and RT. Structural equation modeling analysis showed that RT were strongly associated with K. obovata biomass rather than S. alterniflora biomass, suggesting a strong relationship between RT and the growth of mangrove K. obovata Overall, our study revealed distinct assembly processes of soil AT and RT communities in coastal wetlands, which is crucial for mechanistic understanding of the establishment and maintenance of soil microbial diversity in coastal wetlands under conditions of global environmental changes. IMPORTANCE Coastal wetlands are one of the important ecosystems that play a crucial role in the regulation of climate change. Rare taxa (RT) exist in one habitat along with abundant taxa (AT). In this study, we found that RT exhibited narrower niche breadth and stronger phylogenetic signals than AT. Null model analyses showed that RT were more phylogenetically clustered and primarily governed by homogeneous selection, while AT were more overdispersed and dominated by dispersal limitation. Revealing the differences in the community assembly processes between AT and RT in coastal wetlands is critical to understand the establishment and maintenance of soil microbial diversity in coastal wetlands with regard to environmental changes., (Copyright © 2020 Gao et al.)