Microbial capacities drive waste stabilization and resource recovery in environmental friendly processes. Depending on the composition of waste, a stress-mediated selection process ensures a scenario that generates a specific enrichment of microbial community. These communities dynamically change over a period of time while keeping the performance through the required utilization capacities. Depending on the environmental conditions, these communities select the appropriate partners so as to maintain the desired functional capacities. However, the complexities of these organizations are difficult to study. Individual member ratios and sharing of genetic intelligence collectively decide the enrichment and survival of these communities. The next-generation sequencing options with the depth of structure and function analysis have emerged as a tool that could provide the finer details of the underlying bioprocesses associated and shared in environmental niches. These tools can help in identification of the key biochemical events and monitoring of expression of associated phenotypes that will support the operation and maintenance of waste management systems. In this chapter, we link genomic tools with process optimization and/or management, which could be applied for decision making and/or upscaling. This review describes both, the aerobic and anaerobic, options of waste utilization process with the microbial community functioning as flocs, granules, or biofilms. There are a number of challenges involved in harnessing the microbial community intelligence with associated functional plasticity for efficient extension of microbial capacities for resource recycling and waste management. Mismanaged wastes could lead to undesired genotypes such as antibiotic/multidrug-resistant microbes.

微生物能力在环境友好的过程中推动废物稳定和资源回收。根据废物的成分，压力介导的选择过程可确保产生特定的微生物群落富集的方案。这些社区会在一段时间内动态变化，同时通过所需的利用率来保持性能。这些社区根据环境条件选择合适的合作伙伴，以保持所需的功能能力。但是，这些组织的复杂性很难研究。个人成员的比例和遗传情报的共享共同决定了这些社区的丰富和生存。具有结构和功能分析深度的下一代测序选项已成为一种工具，可以提供与环境利基相关和共享的基础生物过程的更详细信息。这些工具可以帮助识别关键的生化事件并监测相关表型的表达，这将支持废物管理系统的运行和维护。在本章中，我们将基因组工具与流程优化和/或管理联系起来，可将其用于决策和/或扩大规模。这篇综述描述了有氧和无氧两种废物利用过程的选择，其中微生物群落起絮状物，颗粒或生物膜的作用。利用微生物群落智能和相关的功能可塑性来有效扩展微生物资源回收利用和废物管理的能力时，存在许多挑战。废物管理不善可能导致不良的基因型，例如抗生素/耐多药微生物。