Scientific open-source software (OSS) has greatly benefited research communities through its transparent and collaborative nature. Given its critical role in scientific research, ensuring the sustainability of such software has become vital. Earlier studies have proposed sustainability strategies for conventional scientific software and open-source communities. However, it remains unclear whether these solutions can be easily adapted to the integrated framework of scientific OSS and its larger ecosystem. This study examines the challenges and opportunities to enhance the sustainability of scientific OSS in the context of interdisciplinary collaboration, open-source community, and multi-project ecosystem. We conducted a case study on a widely-used software ecosystem in the astrophysics domain, the Astropy Project, using a mixed-methods design approach. This approach includes an interview with core contributors regarding their participation in an interdisciplinary team, a survey of disengaged contributors about their motivations for contribution, reasons for disengagement, and suggestions for sustaining the communities, and finally, an analysis of cross-referenced issues and pull requests to understand best practices for collaboration on the ecosystem level. Our study reveals the implications of major challenges for sustaining scientific OSS and proposes concrete suggestions for tackling these challenges.